If you have your Windows CD, you can reformat the drive via booting up with the CD. However, I highly suggest you completely disconnect your good drive or risk the virus sneaking into it. So plug in the bad one, set your BOIS to boot from the CD as a first priority (instead of the drive), and have at it. It will allow a full format, then you'll be able to use the drive safely as storage.
If you don't have your Windows CD, remove your good drive and put the one with the virus into the computer. On boot up hold down your F8 key until your computer jumps into the "Windows Advanced Options Menu". You'll see a list of boot preferences such as "Safe Mode", "Safe Mode with Networking", etc.
Select the option that says "Safe Mode with Command Prompt". When the prompt comes up, type:
Then hit enter. When the format is done (should only take seconds), you can then safely use the drive as a storage drive.