Drive won't format due to mystery files!

I've got a secondary HD, WD 80g which was originally my primary drive until I installed the RAID0 raptors, during which I diconnected the WD, installed the raptors, OS's software, etc. Only after the system was thoroughly and completely set up and running did I plug the Wd drive back in on the secondary IDE channel. The first thing I did was delete the windows file and programs files, leaving the data files intact (mainly downloads, pictures,and music). Now I want to complete the picture by a reformat of the drive and then optimise it for data storage, mainly the above mentioned type files.
I 've deleted every file that shows on Windows Explorer, with the exception of 'documents and settings/user/"me"/, which in explorer is shown as an empty file. However, when I go to delete it, I get an error message saying the "file is in use and canot be deleted until the program using it is stopped." when I go to reformat, it says the same thing. Explorer shows the harddrive empty except for the above referenced files, however, if I go to 'properties' for that drive, there's a 12+g slice of data unaccounted for, or shown as in use.
I've checked show all files including hidden files and folders. Any idea on how to see what's residing on this disk and how do I get it reformatted?

get the disk that came with the WD drie and perform a low level format (put disk in, reboot, and format). after that you can convert it to whatever file system you want in windows

Are you formatting in Windows?

I'd try using FDISK on a boot floppy rather than Windows as it will not look at any files on the disk, it should just wipe it for you.

Instead of using any other utility why not try to reformat it in the Recovery Console? Boot into the recovery console & type FORMAT X: /U were X is the drive letter of your "storage" disk.

Sonny said:

Instead of using any other utility why not try to reformat it in the Recovery Console? Boot into the recovery console & type FORMAT X: /U were X is the drive letter of your "storage" disk.

Click to expand...

you have to first install the recovery console or boot to cdand sit through the initail setup loading which takes forever... plus he should ahve the disk.. and what better than to use the utility for the drive itself? using windows would be the "3rd party utility" here after-all

Thanks for the input guys. I ran 'chkdisk' on and as soon as it came out of that, i opened explorer and went to reformat. It took it this time. I don't know why it gave me so much trouble before. My only guess is that it might've seen the "ghosts" of the old Windows install and not wanted to reformat out of fear of corrupting itself.
Now I get to go through and move the files off the RAID and clear up some space on it for programs.