This ought to be in Helproom but, here's a starter.
How long is it since your last defrag or, if you've never defragged how old is your machine?
If your hard drive is heavily fragmented it can take a very long time to carry out any cleaning of the drive and I've heard of some drives taking nearly a whole day to complete the job.
If you think that the Windows defragmentation utility is not doing its job properly, I find this click here is excellent. You can get a thirty day free trial but, I was so impressed, I bought a site licence.