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?
There is an abundance of ways untrusted files could cause harm to your system.
One popular way to verify if any single file is malicious is to use Virus Total: http://www.virustotal.com/
Short of re-installing everything from trusted sources you cannot get 100% assurance everything is clean.
If you really, reallyreally, reeheeeelly need those files - and I urge you to rethink that - defintely don't try to access them from a regular machine, but use a clean, throwaway machine you can load up on AV and forensic tools, and then trash it later. Make sure you're fully up to date, and running with minimal privileges. Run at least two AV scans on it, and manually check the files on the temp machine (i.e. if these are java source files, LOOK at them. READ the code.) Try not to restore anything more complicated.
Oh, and don't call it backups, if you took them AFTER the damage was done :).