Yeah, if its got a virus on it though, and you've tried running antivirus programs to get rid of it, then don't back up .exe files, as these would have the virus on to repeat the whole thing again!
A virus works by copying itself, rather than any other computer bug which can just be a file somewhere.
As they have the cabaibility of storing themselves inside EXE files of any type, so don't at all store any.
Documents are fine, as is music and saved files.
If you have an updated virus checker, scan the secondary drive, does it notice any?
Try this, AVG Antivirus (its free):
I hope this helps.