Dealing with a malware-infected external medium is dangerous, but not horrifically so. If there are files on that media that you need to get your hands on, you can get them. You just have to do it cautiously.
One simple solution is to access it on a Mac or a Linux PC. Malware tends to be OS-specific, so it's unlikely to cause harm.
If you're going to use a Windows PC, update your security software first. Then install some extra malware fighters, such as the free versions of Malwarebytes' Anti-Malware and SUPERAntiSpyware. Update those, too.
You don't want Windows to launch a malicious program as soon as you insert the disc or flash drive, so disable AutoPlay. That's the Windows feature that looks for, then runs, instructions on just-plugged-in external media. You can always turn it back on later, although many security experts advise that you don't.
If you're using Windows XP, you'll need to use Tweak UI, a free Microsoft Powertoy, to change this setting. Once you've installed and opened the program, navigate its left pane to My Computer, AutoPlay and Types. Uncheck either Enable Autoplay for removable drives or Enable Autoplay for CD and DVD drives.
Windows 7 and Vista users have it easier. Click Start, type autoplay, and press ENTER. Uncheck Use AutoPlay for all media and devices.
Now you can safely insert the suspect media. But don't open or move any files on it just yet. Instead, scan the disc or drive with every antivirus and malware scanner you've got. You want to determine whether the files you need are infected, and if so, if they can be cleaned.
Once you've determined that the files you want are safe, copy them to your hard drive.
But what do you do with the media after you're done with it? You don't want someone to inadvertently use it and infect their system. At least I hope you don't.
If it's a CD or DVD, rub it against sandpaper or pavement, or cut it into pieces with a pair of scissors. Don't try breaking it with your hands, that can cause dangerously sharp shards flying.
You can securely wipe a flash drive with any number of programs. I recommend the free Eraser. It offers quite a few erasure methods, many quite time consuming, but in this case I'd go with one of the single pass options. You don't need anything fancier.