My Windows PC was recently infected with malware, so I'm planning a completely clean Windows installation. An internal HDD and an external HDD were connected while the infection may have been active, and they contain personal files such as STL 3D-printing files, videos, photos, documents, Adobe presets, ZIP archives, and other backups. Could malware have copied itself onto either drive and infect the new installation when I reconnect them? What is the safest way to check and use these drives afterward?
3 Answers
Your STL files, photos, and videos are relatively low risk as data files, although any file type can theoretically be weaponized if opened by a vulnerable application. Keep the drives disconnected during installation, install updates and security software first, then scan them before using the contents. If the files are irreplaceable, make a backup of the untouched data and consider scanning it from a separate trusted computer as well.
That collection is mostly non-executable data, so the risk is fairly low if you scan first and don’t launch unknown files. Be especially careful with anything ending in .exe, .msi, .bat, .cmd, .js, .vbs, or with documents that contain macros.
A clean Windows install should be done with the internal and external data drives disconnected. After Windows is installed and fully updated, connect the drives without opening files and run a scan with Windows Security, preferably including an offline or second-opinion scan. Photos, videos, and STL files generally aren’t executable, so they normally can’t infect Windows just by being stored on a drive. The bigger risks are executable files, scripts, shortcuts, macros, and files inside archives. Don’t run anything suspicious, and reformat a drive if you don’t need to preserve its contents and want maximum certainty.
Simply plugging in a drive usually isn’t enough for modern Windows malware to run automatically, but a malicious program could be stored there and launched later. Treat ZIP files and documents cautiously, enable file-extension visibility, and avoid opening unknown programs or scripts. If the infection was serious or you cannot identify what happened, copy only essential personal files after scanning and wipe the old drives before restoring them.

The clean Windows 11 installation is finished, but I’m still nervous about reconnecting the drives because most of the contents are STL files, videos, presets, and ZIP archives.