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How is the raid configured?
Any files that aren't executable are fine in most cases.
Usually you can leave the second drive intact and it should be alright, just run a full virus scan over it after you do a fresh install and remove any infected files. It would only really be an issue if the particular virus you got infects other executable/file types. Most malware/viruses these days just dump an executable or a dll or 2 in a few different spots, then add themselves into the computer start up via a few different spots. So most of the time other partitions / drives are fine. But it depends what you were infected with and what it does.
NOD32 is one of the best desktop virus engines around at the moment.
The free version of AVG isn't too bad seeing as its free, but if you are happy to spend money (cough or find it another way...cough...) then NOD32 is the winner.
Don't use anything made by Symantec if you like your computer to perform well, and it doesn't tend to find any viruses anyways... POS.
Also you can run "online" virus scans using free online scan engines.
http://housecall.trendmicro.com/
http://www.bitdefender.com/scan8/ie.html
http://www.kaspersky.com/virusscanner
I recommend those ones for online scanning.
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