How do you run a virus/ malware scan on Gen3 Time Capsule

My late 2010 MacBook Pro was completely wiped out the other day, and a friend of mine who is a techie determined that something completely everything. I mean everything! No boot function...nothing!
I was hoping it was just a HDD failure, since I've had it replaced once before. I noticed before the crash, when I ran "repair disc," then "verify disc" that all these error messages came up. I called Apple Care, and he made me an Apple Genius appointment that day at my nearest store. Long story short, he could not do anything more, since once he removed the casing, he noticed what could have been a liquid spill, which of course, voids Apple Care. Thank God my friend is a tech wizard.
He took it home with him, completely took it apart, rane various hardware diagnostics on it, there was no liquid spill, the HDD does work, the logice board isn't damamged, it was just wiped out.
My Mac was acting funny the last few days, and the fan kept running constantly, so as a precaution I backed everything up to the Time Capsule and another portable hard drive. So the problem is, if I downloaded something and it's now just waiting in one, if not both, of those backups, how can I make sure it doesn't get transfered over once I restore all my files?
Thanks.
Mike

It's most likely not due to any malware infection.
http://www.thesafemac.com/mmg-infected/#spam
If you still want to do a scan, then a good bet is to get the free Sophos. But be warned, no A-V will find everything (definitions for any particular infection first have to be in the A-V catalog), and it may turn up false positives.

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