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Recently had a virus, can I use backed up files on clean system?

I had to reinstall my OS (windows) recently due to a virus. I backed up my source files onto a flash drive. How can I get to those files without problems? I know flash drives can have nasty things in the autorun, but let's say I put the drive on a linux machine and try to read the files off of it, would that be ok? What could actually be embedded within the files themselves that could hurt my new, clean install?