Keep in mind that a formatted HD is going to be smaller than the advertised capacity. For example, a formatted 60 GB might yield 57 GB. That's just the nature of the file system. That being said, if you're on Vista or XP, you can simply go into Control Panel > Disk Management, and then click on your hard drive. It will show up as a logical drive, and if it's partitioned, you'll see the D drive as a partition there. If it's physical, there will be two separate drives listed as logical drives.
You can quick format Drive D and it will wipe all of those hidden files.