Caution Screen Concept

Some people spend hours — maybe even days — trying to clean an infected Windows system and ensuring it’s actually clean and safe afterward. It’s usually not a good idea to do this — just reinstall Windows and start over.

This may seem like a daunting task, especially if you don’t have good backups of your important files. But it’s worth it to quickly obliterate an infection and ensure your system is safe.

If One Piece of Malware Slips By, Your Computer is Compromised

RELATED: How to Remove Viruses and Malware on Your Windows PC

The key to securing your computer is ensuring it doesn’t get infected in the first place. That’s why people run antivirus applications that can check programs before they run, ideally preventing a piece of malware from running even once. If malicious software makes it through this protection, it has free rein over your system until it’s discovered and removed.

This is a problem for many different reasons. The malware can take this chance to burrow deeper into your system, hiding itself from being discovered by installing a rootkit that starts up during the boot process. It can infect various system files. It can use its access to transmit your personal data, credit card numbers, and passwords over the Internet.

Worse yet, malware can function as a Trojan horse, opening the floodgates to additional malware that it will download and install from the Internet. If you find your computer is actually infected by a piece of malware, you don’t know if that’s the only piece of malware that’s infected your computer.

Antivirus Utilities Aren’t Perfect, and Can Take Time

RELATED: How to Use An Antivirus Boot Disc or USB Drive to Ensure Your Computer is Clean

Antivirus utilities aren’t perfect. To really clean up a system, you’ll want to run an antivirus boot disc to scan your Windows system for malware and try to remove it all — or at least reboot into safe mode. This scan process takes some time, and it isn’t guaranteed to be 100 percent successful. If your system is infected and the anti-malware software found and removed an infection — or, even more worryingly, multiple infections — there’s no guarantee your system is completely safe.

To mitigate this problem, you might want to run multiple different antivirus programs, scanning your system with those multiple engines to get a second, third, and maybe even fourth opinions. This takes more and more time, and you’ll never be 100 percent sure everything is gone, and your system is completely secure.

Fix Any Infection By Reinstalling Windows

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Reinstalling Windows is the solution. If a computer is seriously infected — not just by a shady Ask toolbar or the browser cookies many silly security programs consider a “threat,” but by actual malware — we recommend starting over from a fresh Windows system. To do this, you just need to use your manufacturers’ recovery partition to restore your Windows system, reinstall Windows from disc or USB drive, or use the Refresh your PC feature found in Windows 8 or 10.

When you reinstall Windows, your system files will be wiped and they’ll be replaced with known-good ones from the Windows installation disc. You’ll also have to install your programs again, which will ensure they’re safe, too. This takes a bit of time, but perhaps not as much as you’d think — especially if you have good backups. It can also save time over long, arduous slog of cleaning an infected PC and triple-checking it.

Ensure you have backups of your important files before doing this! Some methods of reinstalling Windows won’t wipe your personal files, but it’s always good to be safe.

How to Quickly Back Up Your Important Files

RELATED: How to Use a Windows Installer Disc to Back Up Your Files When Your Computer Won't Boot

If you keep good backups, you’re good to go. If not, you’ll want to back up your important files first. You probably shouldn’t do this while the infected system is running. Instead, we recommend booting from a Linux live CD or USB drive and using that clean system to copy your important data files to a USB drive. Believe it or not, you can also back up your files directly from a Windows installer disc if you have one lying around!

You’ll then have a backup, and you can copy the files from your backup to your fresh Windows system after reinstalling Windows.

Ensure Your Backups Are Secure

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You’ll want to ensure all your backups are clean and uninfected, of course. Generally, the files to watch out for are the .exe files and other executable programs. These can be infected by viruses and infect your system later. Microsoft Office files could also potentially have malicious macros inserted into them, but modern versions of Office are more resistant to this. Other data files like images, videos, and music generally can’t be infected.

It’s a good idea to eye and .exe files with suspicion if they came from an infected computer. Re-download them if possible to ensure they’re safe. You’ll also want to run a scan of your backup files with an anti-malware program after getting a fresh system, ensuring nothing nasty is hiding in your backups somewhere.

This may sound like a Herculean task for people who don’t keep good backups and are worried about setting up their computers from scratch. But, if you do anything sensitive with your computer, from online banking and shopping to filing taxes with your social security number, it’s better to be safe than sorry. You won’t be worrying whether your computer is still infected in a week or two.

Profile Photo for Chris Hoffman Chris Hoffman
Chris Hoffman is Editor-in-Chief of How-To Geek. He's written about technology for over a decade and was a PCWorld columnist for two years. Chris has written for The New York Times and Reader's Digest, been interviewed as a technology expert on TV stations like Miami's NBC 6, and had his work covered by news outlets like the BBC. Since 2011, Chris has written over 2,000 articles that have been read more than one billion times---and that's just here at How-To Geek.
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