You have just done a major clear out of your drives! Have you run "Defrag" on each one? Your files may be scattered, [Fragmented] all over your drives and this will put them back together again.
If you download music or other files, you may have picked up a virus. Do you have up to date anti-virus on your system? If not, then a good free one is AVG click here and this is also a good program to have for sorting out and removing spy-ware. click here j.