then how would i erase everything besides the boot files, windows included on the C drive? so then i can start over with a format and a brand new instillation of windows? ... but still be able to boot up the computer and run from the windows installed on the E drive.
I'm not sure quite why you want to keep the separate installation on the E: drive which complicates the issue somewhat. However, you could open the case, and remove (or disconnect) the E drive temporarily, then use Darik's Boot and Nuke (DBAN), which has a separate forum on the Board, to erase drive C completely. You can then reconnect the E drive; you might need to change the BIOS settings to make it the bootable drive, and it will become drive C in Windows, which might be a nuisance. Also it must have a master boot record which refers to the Windows installation it contains, or it will not boot.
Another approach might be to use an imaging program to back up both drives to a separate - e.g. USB - drive (so you can get files or folders you might need back again), then use DBAN to clear both drives, so that you can start again. This is more work, but you usually get a better running Windows installation, and it gives you the opportunity to get rid of all the stuff that seems to accumulate over the years. Another variant on this theme (which might be what you want) would be
- Disconnect Drive E;
- Use DBAN to Clear Drive C;
- Install Windows on Drive C from the Windows install or computer recovery disk; you will need manufacturer's instructions on the latter;
- When the Windows installation is stable (drivers etc. are installed), reinstall Eraser;
- Connect the E drive;
- Copy any files you want to keep from the E Drive to the C: drive (or make a drive image so you can recover what you want);
- Erase the files then wipe the free space on the E drive.
If you prefer this approach, be warned that Windows Explorer has a little known but very bad habit of failing or even corrupting when copying very large numbers of files. For that kind of operation, I use the Microsoft SyncToy, or a drive imaging program as aforesaid.
If you don't fancy using DBAN (which some people, for understandable reasons, find pretty scary), and you have access to another computer and a USB hard drive caddy, put one of your drives in the caddy, install Eraser on the other computer, then connect the caddy and use Eraser first to erase the files on the drive, then clear the free space. If you leave the Windows installation on Drive E, the points I made in my first paragraph will also apply. You can also use this technique as a variant of the backup -> clear -> reinstall -> restore sequence I have outlined. It is also the best technique to use if you have a recovery partition on either drive that you wish to keep; if DBAN finds such a partition, it will happily 'nuke' it.
Whatever tool you you use, the process of erasing files then free space on a drive is very lengthy - many hours, even a whole day, is quite typical.
If anything doesn't make sense, please ask again.