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clean out the system (it was time for it anyway) I would like to re-install windows.
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You don't even have to use something as extreme as killdisk, it's enough to format the hard drive during the install - aka, during the installation process, don't just reselect the old partition, but delete it and create a new one in it's place. You can even create multiple partions, such as one for Windows, and one for other data (music, CAD data, movies, applications...), and when you reinstall, you can only reformat the Windows partition, leaving all your other data. (Of course, this doesn't prevent fragmentation and other shortcomings of NTFS...)
However, if you don't format the hard drive, windows will write its over the preexisting files, and all the pre-re-installation junk is left. Formatting the hard drive means you start with a clean slate.