We have suggested a couple of options in the staff area, I will list them here and you can choose which you feel most comfortable with.
My route would be to 1st make sure ALL protection is fully updated, do NOT allow the drive to auto run (turn that off first), then connect it but do NOT enter it, bring up your "My Computer" where you should see it (assuming it doesn't want a reboot to finish installing drivers for it), then right click on it and run the protection if you wish to clean it up first, or if going for a straight wipe then I suggest using
HDD Low Level Format Tool.
BUT,
Be Warned, this is an extremely powerful and unforgiving tool, it is a windows based format tool, and it WILL wipe your OS drive if you select the wrong drive to format, and yes even though your using the OS drive to run the tool, it will still format that drive without confirmation the second you tell it go, so triple check the drive you tell it to wipe, but this is the best tool IMHO if it's a really nasty infection.
Another suggestion from Ztruker is to use DBAN (Darik's Boot and Nuke), I am not used to this tool so can't say much about what to do, but he suggested putting this on floppy or disk then unplugging the hard drives of the system that will be used to do this, then boot to this tool and format, this appears the better idea on paper because your drives are never connected at the time this USB one is, but that said if this is a memory resident virus involved it could save itself to the system memory and infect your drives once you connect them back up.
The thing to remember with these things is that no matter how you try, there is ALWAYS risk, there is no way round that, BUT, that said I have used the method I suggested many times without issue, as I dare say Ztruker has with his, all we can do is minimise risk, but the only way to take away the risk is not to do it, but IMHO either of these methods should be as safe as you can get without going to extremes, please take your time to think about these options, and ask for any input you need to give you the best info possible before you start, this should give you a trouble free solution.
*edit
OK I have been doing some experimenting, as it happened I needed to reinstall my daughters system, so I took the opportunity to try this DBAN option, and it's the 1st time I've ever been able to run this program, previous attempts on the UBCD disk have failed for me, but what you need is v1.07, it has to be the
dban-1.0.7_i386.exe file, save that to your desktop and run it with the floppy or thumb drive in, select which you're wanting to use from the drop down box, then click on install and it will install the required files to your selected media.
Once you have done that you will need to enter your bios and change your boot order to the media you have chosen, alternately if your system has an option to press a specific key to select what to boot from then thats even better if it allows the media chosen, once the program has loaded follow the on screen prompts, select the external drive, BUT, we can't be certain if it will allow this or not, info that Ztruker has come across seems to suggest it's hit and miss, so some can, others can't, but you should be able to see quickly enough if the drive is shown, if it is then you can format using this, but it is extremely slow, so if you go this route it may take many hours to complete, so running it overnight may be a wise option for this, hope it helps anyway.