Alan, are you asking how to purge the MFT of non-used entries?
If you're looking to clear out the MFT you need to compact and compress it back to what it would be like when a new disk is formatted, but of course keeping the existing valid-in-use entries. The MFT only grows, NTFS/Windows never shrinks it on its own.
When you delete a file you mark a spot (in the mft) as being open) and when you create a new file, that spot (or others nearby) can be used to store the new location information. In the meantime, in that spot rests the previous filename of what you just deleted, and some of the location data!
Let's say you format a disk fresh. It now has only 10 MFT entries (an arbitrarily low number I made up). And as you add your music collection it goes to 5,000 entries. Then 23,456 entries with your photo collection. And up and up. If you decide to delete your music collection the count still remains at 23,456. Those 5,000 music spots would now get filled with CCleaner's zzz.z.z..zzz.zz files.
And since they were made and deleted, the zzz.z.z..zzz.zz entries are remant spots earmarked for re-use when you start creating files again. What used to be validfilename-1.mp3 validfilename-2.mp3 and so on and so forth are now zzz.z.z..zzz.zz. (after drive wipe).
What you need to do is remove any MFT entries that are un-used, by way of concatenating the branches of the MFT's B+ tree's structure and reconnecting the structure together over the open spots - those zzz.z.z..zzz.zz entries otherwise known as recently deleted entries. And as a result you have no filler space where stuff is hiding. And in the process you're shrinking the MFT down to size as a natural result.
The plain english analogy is compacting the dead air space out of something until only real substance remains. When CCleaner's drive wipe is used, it only fills the holes with unidentifiable grey "stuff". It does nothing to remove the holes and old content.
I hope that makes sense to you?
