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When a file is deleted from the hard drive and the free space it used to occupy is securely overwritten (wiped), recovery tools can still usually find the file was there and show its name. As far as I understand this is because some data about old files is left in MFT area. How to eliminate this?

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possible duplicate of Is there a program to truly delete all deleted files? – Ƭᴇcʜιᴇ007 Mar 7 '11 at 4:00
I've found CCleaner to offer "Wipe MFT Free Space" option, but haven't tested this yet... And I am pretty sceptical about it to help... – Ivan Mar 10 '11 at 14:00
I believe that option will do exactly what you are looking for. – grawity Mar 24 '11 at 17:15

Short answer, it is not possible.

The MFT is a complex dynamic table file at the heart of the NTFS. To change one small part of it, corrupts the whole drive.

MS isn't telling how it is structured, and no one is going to risk putting out a application on a trial and error basis, that 'cleans' the file names, if there is any chance it will destroy the system.

(Oh yes, insert negative comments about MS exposing peoples data here.)

So depending on the pros and cons, you may want to restart with a fresh install, and then use less sensitive file names and use secure deletion at the recycling bin. Use TrueCrypt containers to keep files separate from programs. Perhaps FDE (Full Disk Encryption) is a option if it is that important.

To make things clear to others, it is not what Ccleaner and the others do, drive wiping the MTF and defragging it and all the rest doesn't clean the MFT names. They overwrite the file spaces in the MTF, but the names remain. It is the deletion of the FILE NAMES ONLY that the OP is asking about. (File names that can only be seen with specialized file recovery applications)

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I've used the MFT wipe free space with CClean. (It does take forever, up to several days.)

Before running wipe, I could easily get a full list of previously deleted files with Recuva, despite the files being several years old and overwritten multiple times beyond recovery. This is because Recuva takes the list of files from MFT. (Unless you run the deepscan, which actually goes through the disk, seeing what's in there. This also takes forever, however.)

After running MFT wipe free space with CClean, Recuva finds nothing. Not without deepscan anyways. Therefore, I'm fairly certain CClean also takes MFT into account whilst wiping.

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First, check how many files Recuva reports that can be recovered. Say it is 1001.
Open a command window and create a temporary directory. Change to that directory.

MKDIR C:\TempReco
CD C:\TempReco

Create at least 1001 files in this directory using the command below with proper parameters.

FOR /L %i in (1,1,1001) do echo willdelete>file%i.tmp

When this completes, delete the files with either from command window or by locating with Windows Explorer. Then, empty the Recycle Bin.
When you check again with Recuva, it will only show filenames you have just deleted.

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In case Windows does not clean unused space when storing a new name in an MFT record, you may want to use a longer name in the 'file%i.tmp' template, like 'atleastfirst80charactersofdeletednamesshouldbecleared%i.tmp'. – Burhan Oct 7 '15 at 14:30

I think Paragon Hard Disk Manager Suite (Pro?) can help you do this by shrinking the MFT:

As the $MFT grows, it will occupy the increasing amount of space in the MFT Zone, and the current size of $MFT is totally unrelated to the size of the MFT Zone.
When one executes the "Compact MFT" (also may be called “Shrink MFT” in some editions) operation, the $MFT itself will be shrinked, but the MFT Zone will remain intact - just a block of reserved free space.

It can shrink the MFT, which means deleted file records won't be there anymore.

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Revo Uninstaller freeware wipes the MFT almost completely. Tested on formated WD 500GB with AVG PC tuneup utility to view the MFT size before Revo Unistaller and after Revo Unistaller. MFT almost completely gone while before it was enormous.

Go to Tools --> Tracks Cleaner --> Evidence Remover --> select drive and run it.

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