Why don't you just not act on the found viruses if you know they are not? After a Virus scan, the program should not automatically clean things out, but rather stop and say "found these issues, what do you want to do". Or at least you can configure it to do that.
Truecrypt is also a good thing to learn to use, and will keep the scan from that directory. Although you'd need to unmount the encrupted volume when you do the scan or it will pick up the files anyway unless you set the scan to only run on certain drive letters.