Tuesday, September 2, 2025

Windows PC Clean-up and Tune-up Guide - 2025 Update

 


Full & Complete Windows PC Clean-up Guide

Overview

This guide provides a systematic approach to cleaning, securing, and optimizing a Windows PC using both built-in tools and trusted third-party utilities. Follow these steps in order for best results.

Prerequisites

  • Administrator access to the Windows PC
  • Stable internet connection for downloads and updates
  • Create System Restore Point before beginning


Phase 1: Initial Assessment & Software Management

Step 1: Uninstall Obvious Bloatware

Target Programs for Removal:

  • "Free Trial" software that's expired or unwanted
  • Obvious junk programs and toolbars:
    • One Search, Driver Support, One Bar
    • PC optimization "scareware"
    • Fake antivirus programs
    • Browser hijackers and toolbars
    • Outdated or redundant software

Removal Process:

  1. Control Panel: Programs and Features
  2. Windows Settings: Apps & Features (Windows 10/11)
  3. Review Carefully: Research unfamiliar programs before removing
  4. Use Browser Hijack Reference: Consult reputable sources for malicious adware identification

Step 2: Install/Update Essential Programs

Use Ninite.com for Efficient Installation: Visit ninite.com to create a custom installer package for:

Essential Browsers (Update if installed):

  • Chrome
  • Firefox
  • Microsoft Edge (built-in, check for updates)

Required Runtimes:

  • Java Runtime Environment (latest version)
  • Microsoft .NET Framework (latest version)
  • Microsoft Visual C++ Redistributables
  • Adobe Flash alternatives if needed

Security Tools:

  • Malwarebytes Anti-Malware
  • Malwarebytes ADWCleaner
  • BleachBit

Phase 2: Security Scanning & Malware Removal

Step 1: Malicious Software Removal Tool (MRT) Scan

Running MRT Scan:

  1. Open Run Dialog: Press Win + R
  2. Launch MRT: Type mrt and press Enter
  3. Choose Full Scan: Select comprehensive scan option
  4. Start Scan: Click "Next" and let the scan complete
  5. Review Results: Check summary and follow removal recommendations
  6. Restart if Required: Reboot the system if prompted

Step 2: Windows Defender Full System Scan

Performing FULL Scan (Not Quick Scan):

  1. Open Windows Security: Press Win + I → Update & Security → Windows Security
  2. Virus Protection: Click "Virus & threat protection"
  3. Scan Options: Click "Scan options" under Quick scan button
  4. Select Full Scan: Choose "Full scan" radio button
  5. Start Scan: Click "Scan now"
  6. Wait for Completion: Full scan may take 1-3 hours
  7. Address Threats: Follow Defender's removal recommendations

Step 3: Malwarebytes Anti-Malware (MBAM) FULL Scan

Installation and Setup:

  1. Download: Visit malwarebytes.com
  2. Install: Run installer with administrator privileges
  3. Update Definitions: Allow MBAM to download latest signatures

Running FULL MBAM Scan with Rootkit Detection:

  1. Launch MBAM: Open from desktop shortcut
  2. Scan Settings:
    • Click "Scan" tab
    • Select "Threat Scan" or "Custom Scan"
  3. Enable Rootkit Scanning (Critical):
    • Check "Scan for rootkits" checkbox
    • This significantly increases scan time but improves detection
  4. Configure Custom Scan (if selected):
    • Click "Configure Scan"
    • Enable "Rootkit Detection"
    • Select all drives for comprehensive coverage
  5. Start Full Scan: Click "Start Scan"
  6. Scan Duration:
    • Standard scan: 15-45 minutes
    • With rootkit scanning: 1-3 hours
  7. Quarantine All Threats:
    • Review detected items carefully
    • Click "Quarantine" to remove threats
    • Restart when prompted (required after rootkit removal)

Step 4: ADWCleaner for Adware and Browser Hijack Removal

Running ADWCleaner:

  1. Download: Get from malwarebytes.com/adwcleaner
  2. Run as Administrator: Right-click and select "Run as administrator"
  3. Accept License: Agree to terms of use
  4. Start Scan: Click "Scan Now"
  5. Wait for Completion: Scan typically takes 5-15 minutes
  6. Review Results: Examine detected adware and PUPs
  7. Clean & Repair: Click "Clean & Repair" to remove all detected items
  8. Restart System: Reboot when prompted to complete removal

Step 5: Rootkit Check for Heavily Infected Systems

When to Use TDSKiller:

  • System shows signs of heavy infection
  • Multiple security tools detect persistent threats
  • System behaves erratically despite previous cleaning attempts

TDSKiller Usage:

  1. Download: Get TDSKiller from Kaspersky Rescue Disk
  2. Run as Administrator: Launch with full privileges
  3. Scan: Perform full rootkit scan before other cleaning procedures
  4. Remove Threats: Follow removal recommendations
  5. Restart: Reboot system before continuing with main cleanup


Phase 3: Browser Cleanup & Optimization

Comprehensive Web Browser Cleanup

For Each Installed Browser (Chrome, Firefox, Edge):

1) Check Extensions/Add-ons:

  1. Chrome: Menu → More Tools → Extensions
  2. Firefox: Menu → Add-ons and Themes
  3. Edge: Menu → Extensions
  4. Remove Suspicious Items:
    • Unknown or unrecognized extensions
    • Toolbars and search helpers
    • Extensions from untrusted developers
    • Anything installed without your knowledge

2) Check Browser Settings:

  1. Homepage Settings: Verify startup page hasn't been hijacked
  2. Default Search Engine: Ensure it's your preferred choice
  3. New Tab Page: Check for unwanted modifications
  4. Download Settings: Verify download location is secure

3) Reset if Necessary:

  • Chrome: Settings → Reset and Clean Up → Restore settings to original defaults
  • Firefox: Help → Troubleshooting Information → Refresh Firefox
  • Edge: Settings → Reset Settings → Restore settings to default values

4) Additional Browser Security:

  • Clear browsing data (cache, cookies, history)
  • Update to latest version
  • Enable automatic security updates
  • Review and update saved passwords


Phase 4: System Cleanup and Optimization

Step 1: BleachBit Junk File Cleanup

Installation:

  1. Download: Visit bleachbit.org
  2. Install: Run installer as administrator
  3. Runtime Requirements: Install Visual C++ 2010 Redistributables if needed

BleachBit Configuration (Specific Settings):

  1. Launch as Administrator: Essential for system-wide cleaning
  2. Enable These Cleaning Options:
    • System → Temporary files
    • System → Recycle bin
    • System → Prefetch
    • Web Browsers → Cache (for all installed browsers)
    • Windows Defender → Quarantine files
    • Windows Defender → Log files
    • Windows Explorer → Thumbnails
    • System → Memory dump files

Running Cleanup:

  1. Preview First: Click "Preview" to see what will be cleaned
  2. Review List: Examine files to be deleted
  3. Execute Cleanup: Click "Clean" to proceed
  4. Monitor Progress: Watch cleanup process complete

Step 2: Paging File Optimization

Setting Virtual Memory:

  1. Access Settings: Settings → System → About → Advanced System Settings
  2. Performance Settings: Advanced tab → Performance section → Click "Settings"
  3. Virtual Memory: Advanced tab → Virtual Memory section → Click "Change"
  4. Configure Paging File:
    • Uncheck "Automatically manage paging file size"
    • Select "Custom size"
    • Set Initial and Maximum Size:
      • Option 1: 1.5 times your RAM amount (e.g., 16GB RAM = 24GB paging file)
      • Option 2: Set to 4096MB (4GB) for most systems
  5. Apply Changes: Click "Set" → "OK" → "Apply"
  6. Restart Required: Reboot to apply changes

Step 3: System Performance Optimization

Visual Effects Optimization:

  1. Access Performance Options: Right-click "This PC" → Properties → Advanced System Settings → Advanced tab → Performance Settings
  2. Custom Settings: Select "Custom"
  3. Enable Only These Visual Effects:
    • ✅ "Use visual styles on windows and buttons"
    • ✅ "Smooth scroll list boxes"
    • ✅ "Smooth edges of screen fonts"
    • ✅ "Show translucent selection rectangle"
    • ✅ "Use drop shadows for icon labels on the desktop"
  4. Disable All Others: Uncheck remaining options for better performance
  5. Apply Settings: Click "Apply" → "OK"

Startup Program Management:

  1. Open Task Manager: Press Ctrl + Shift + Esc
  2. Startup Tab: Click "Startup" tab
  3. Review Startup Items: Examine all programs
  4. Keep Essential Programs:
    • OneDrive/Microsoft Office applications
    • iCloud Drive (if using Apple devices)
    • Printer software
    • Wi-Fi management software
    • Audio/Video drivers and software
    • Specialty applications (Garmin, Fitbit, etc.)
    • Antivirus software
  5. Disable Unnecessary Items:
    • Gaming software (unless frequently used)
    • Update checkers for non-critical software
    • Bloatware and trial software
    • Unknown or suspicious programs


Phase 5: System Analysis &Advanced Security

Step 1: Autoruns Analysis with VirusTotal

Download and Setup:

  1. Download: Get Autoruns from Microsoft Sysinternals
  2. Extract and Run: Launch autoruns.exe as administrator

VirusTotal Integration:

  1. Enable Scanning: Options → Scan Options → Check "Check VirusTotal.com"
  2. Submit Unknown: Optionally enable "Submit unknown executables"
  3. Accept Terms: Agree to VirusTotal terms of service

Analysis Process:

  1. Wait for Results: Allow VirusTotal scanning to complete
  2. Review Color Coding:
    • Red/Pink: High risk detections
    • Yellow: Medium risk or unsigned files
    • Green: Clean files
  3. Focus on Key Areas:
    • Logon tab: Startup programs
    • Services tab: System services
    • Network Providers: Network-related startup items
  4. Investigate Suspicious Items: Research unknown or unsigned executables

Step 2: Process Explorer Monitoring

Setup and Configuration:

  1. Download: Get Process Explorer from Microsoft Sysinternals
  2. Run as Administrator: Launch procexp.exe with admin privileges
  3. Enable VirusTotal: Options → VirusTotal.com → Check "Check VirusTotal.com"

Active Monitoring:

  1. Real-time Process Analysis: Monitor running processes
  2. VirusTotal Checks: Right-click processes → "Check VirusTotal.com"
  3. Investigate Anomalies:
    • High CPU usage from unknown processes
    • Processes in unusual locations
    • Network activity from unexpected programs
    • Unsigned executables with suspicious behavior


Phase 6: Windows Updates & Final Optimizations

Step 1: Complete Windows Updates

Update Process:

  1. Access Windows Updates: Settings → Update & Security → Windows Update
  2. Enable Microsoft Updates:
    • Click "Advanced options"
    • Enable "Receive updates for other Microsoft products"
    • Enable "Show a notification when your PC requires a restart"
  3. Check for Updates: Click "Check for updates"
  4. Install All Updates:
    • Download and install all available updates
    • May require multiple update/restart cycles
    • Some updates may fail initially but resolve in subsequent cycles
  5. Verify Completion: Ensure all current updates and upgrades are installed

Update Best Practices:

  • Allow automatic restarts during maintenance hours
  • Don't obsess over failed updates - they often resolve themselves
  • Prioritize security updates and cumulative updates
  • Keep checking until no new updates are available

Step 2: System File Integrity Check

Running System File Checker:

  1. Open Command Prompt: Run as administrator
  2. SFC Scan: Type sfc /scannow and press Enter
  3. DISM Check: If SFC finds issues, run DISM /Online /Cleanup-Image /RestoreHealth
  4. Review Results: Address any system file corruption found


Phase 7: Final Cleanup & Maintenance Setup

Step 1: Final Disk Cleanup

Windows Disk Cleanup:

  1. Run Disk Cleanup: Type cleanmgr in Run dialog
  2. System Files: Click "Clean up system files"
  3. Select Categories:
    • Windows Update Cleanup
    • System error memory dump files
    • Temporary files
    • Downloaded Program Files
  4. Execute Cleanup: Proceed with deletion

Step 2: Performance Verification

System Check:

  • Boot Time: Verify faster startup
  • Application Loading: Check improved response times
  • Available Storage: Confirm freed disk space
  • Task Manager: Review CPU and memory usage
  • Network Performance: Ensure stable connections


Ongoing Maintenance Schedule

Weekly Tasks

  • Windows Defender quick scan
  • Empty Recycle Bin
  • Check Windows Updates
  • MBAM threat scan (without rootkit scanning for speed)
  • Review running processes in Task Manager

Monthly Tasks

  • Full antivirus scan (Defender + MBAM with rootkit scanning enabled)
  • BleachBit comprehensive cleanup
  • ADWCleaner scan
  • Review and manage startup programs
  • Browser maintenance and extension review

Quarterly Tasks

  • Full system analysis with Autoruns
  • Process Explorer security review
  • System file integrity check (SFC scan)
  • Paging file optimization review
  • Performance settings verification

As-Needed Tasks

  • Immediate rootkit scan if system behaves unexpectedly
  • Browser reset if hijacking is suspected
  • TDSKiller scan for persistent threats
  • System restore if cleanup causes issues

Safety Guidelines and Best Practices

Before Starting Cleanup
  • Create System Restore Point: Control Panel → System → System Protection
  • Backup Critical Data: Ensure important files are backed up
  • Document System State: Note current performance issues
  • Close Running Programs: Minimize interference during scans

During Cleanup Process

  • Don't Rush: Take time to review scan results
  • Research Unknown Items: When uncertain, investigate before removing
  • Keep Detailed Notes: Document what you remove for future reference
  • Monitor System Stability: Watch for unusual behavior during process

Red Flags to Investigate

  • Processes running from temporary directories
  • Unsigned executables with network activity
  • Unexpected high CPU or memory usage
  • Browser settings changing without permission
  • Multiple security programs running simultaneously
  • System performance degrading after cleanup


Troubleshooting Common Issues

False Positives:

  • Research flagged items with multiple sources
  • Check software vendor websites for verification
  • Use multiple security tools for confirmation
  • Restore from quarantine if legitimate software affected

System Instability:

  • Boot to Safe Mode if necessary
  • Use System Restore to previous checkpoint
  • Check Windows Event Viewer for error details
  • Reinstall accidentally removed legitimate software

Persistent Threats:

  • Run TDSKiller for advanced rootkit removal
  • Use Windows Defender Offline scan
  • Consider professional malware removal services
  • Factory reset as absolute last resort


Additional Security Recommendations

Browser Hardening

  • Install reputable ad blockers (uBlock Origin)
  • Enable automatic security updates
  • Use secure DNS providers (Cloudflare, Quad9)
  • Regularly review and clean saved passwords
  • Enable two-factor authentication where available

System Security

  • Keep all software updated automatically
  • Use Windows Defender or reputable antivirus
  • Enable Windows Firewall
  • Regular security-focused maintenance scans
  • Avoid suspicious downloads and email attachments

Performance Maintenance

  • Monitor startup programs quarterly
  • Clean temporary files monthly
  • Defragment traditional hard drives (not SSDs)
  • Monitor disk space usage
  • Keep system drivers updated

This comprehensive guide combines reactive cleanup with proactive maintenance to ensure optimal system performance, security, and stability. Regular application of these procedures will keep Windows systems running efficiently and securely.



Created & Maintained by Pacific Northwest Computers



📞 Pacific Northwest Computers offers remote and onsite support across: Vancouver WA, Battle Ground WA, Camas WA, Washougal WA, Longview WA, Kelso WA, and Portland OR
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