If it's a second hard drive and your computer recognizes it you just right click the disk and pick format. Then pick if you want FAT32 or NTFS. We recommend NTFS.
If you are going to format your main hard drive (C drive) you can do so by booting to your Windows DVD as if you were going to install Windows. Make sure you BIOS is set to boot from CD before hard drive or else it will keep booting into Windows.
After you boot to the CD, Windows will load files and eventually get to a point where it asks where you want to install Windows. From there it will display your hard drive configuration and give you options to leave it as is or format it. Then you can format the disk and cancel the install if that's all you want to do or you can continue installing a clean copy of Windows.
Keep in mind that formatting the drive erases EVERYTHING so back up your files first!