How to restore missing space in NTFS file systems
Solution 1:
Format? That's pretty much the smoothest way of cleaning out a filesystem.. replacing it. :D
If you are storing large files selecting a larger allocation unit will reduce overheads.
I went from about 300MB in the MFT to less than 10MB after formating with a 64K allocation unit and copying back the data. This was on a 250GB NTFS volume.
I'd also look at system restore. Try running WinDirStat as SYSTEM using PsExec and see if there are large files under System Volume Information named Restore{GUID}.
To delete all but the most recent shadow copy for every volume on your system, go to Disk Cleanup, select "Clean up System files", then use the 2nd button on the "More Options" tab.
To clear just one volume disable and then re-enable shadow copies for the volume from the "System Protection" tab of System Properties.
(If you're interested in the size of your MFT, look at the output of defrag /a)
Solution 2:
There is a slight chance the missing space is in NTFS alternate data Streams - use the sysinternals streams utility to find out.
Alternate data streams allows files to be associated with more than one data stream. For example, a file such as text.txt can have an ADS with the name of text.txt:secret (of form filename:streamname) that can only be accessed by knowing the ADS name or by specialized directory browsing programs. Alternate streams are not detectable in the original file's size...
Solution 3:
Two points -
1) I have often seen on client (and my own) computers that when free space gets very low (less than 1%) when files are deleted, they do not free up the appropriate amount of space (delete a 1 gig file, only get 500 MB back).
2) I have never found a way to recover ALL of this space, but I have found a way to recover some, which I will outline below:
Steps to clear out the page file area -
1) Right click on "My Computer" and select properties
2) Click the advanced tab
3) click "settings" under "performance"
4) Click the advanced tab again
5) Under virtual memory, click "change"
6) Set the page file to 0 MB, then "okay" out of all the screens and restart the computere
7) Reset the page file to the appropriate size
That should help clear out some of the missing space.