Sure, download and burn any Linux or BSD distro to CD. Personally, I recommend for doing this the SuSE CDs that have the entire OS, already installed, on the CD so you can boot into Linux and then do work on your harddrives. I don't quite remember the name of it now, but you should be able to find it on their website.
Once you've got that up, you should be able to see both of your drives and format the appropriate one.
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Eat antimatter, Posleen-boy!
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