That many of today's malware, virus, trojan (call them what you will) are now booby trapped. So even if you use an bootable Live Antivirus it may blow up on the next boot.

What this means is such work is now more expensive if the client is not ready for a wipe out. You clone the drive for safety then use a current Live CD (definitions are updated and a new CD issued, not just definitions.)

I think you are trying to run Windows and scan those drives. Given the changes in PCs over the years I think you'll have to use new ways.