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I have just taken off personal files from my hard drive to a back up drive, the drive is now empty of all files including hidden files but is showing 9.3gb of space being used.

My recycle bin is empty and I've just deleted temporary files and I don't encrypt files

Why is that?!

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Well, the OS takes up space! – Dave Jan 7 '13 at 16:51
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I assume that you are not referring to the drive that has your OS installed right? Are there any folders in the drive? What OS are you using? – terdon Jan 7 '13 at 16:54
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this isn't on the main drive and there are no folders there. Its windows 7 – Aasim Azam Jan 7 '13 at 23:13
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If you open an elevated Command Prompt window, type D: <Enter> dir/a/s, what do you see? – Karan Jan 7 '13 at 23:28
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@AasimAzam it is perfectly acceptable on this site to answer your own question and accept it if you figured it out yourself. – Scott Chamberlain Jan 8 '13 at 7:26

I recommend scanning the drive with WinDirStat which will show all your files, including NTFS based-ones.

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Most likely this is from hidden system files like the System Restore Image

Go to your System Properties page by clicking Advanced System Settings from the system info page.

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from there go to your sytem protection tab and check that protection is set to off

enter image description here

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its already all off – Aasim Azam Jan 7 '13 at 23:17

Could be shadow copies... go to My Computer, right-click any drive, go to Properties, and check the Shadow Copies tab.

Also, it could be files in the Recycle Bin, if you deleted something and haven't emptied it yet.

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that is all done – Aasim Azam Jan 8 '13 at 0:35
    
Maybe it's just the MFT and NTFS journal. – Bigbio2002 Jan 8 '13 at 0:36

Probably the pagefile. You can run space sniffer, which is a very lightweight tool that graphically shows the distribution of file usage, in order to verify what's actually being used on the drive: http://download.cnet.com/SpaceSniffer/3000-18512_4-10913555.html

Windows keeps some space on the harddrive (pagefile) which acts like physical memory and it manages that automatically in windows 7. To manage manually click Start and type "View Advanced System Settings"... that opens the system properties window. Click the "settings button int he performance section. Then click the Advanced tab and click "Change" on the virtual memory. There you can change the drive the page file is saved on, but don't go below the recommended amounts.

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I had this problem and was able to resolve by deleting pagefile.sys (as indicated in other responses). ** The key indicator was that I deleted all files on the disk and it still showed as having space used on drive.
** Also, search registry and you'll find a key for pagefile.sys on the target drive

Here is a link with instructions: http://www.techentice.com/delete-pagefile-sys-in-windows-7/ that has the details to find and modify pagefile settings.

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Welcome to Super User. External links can break or be unavailable. It's better to include all of the essential information within your answer and use the link for attribution and further reading. Thanks. – fixer1234 Apr 20 at 18:56
    
Please quote the essential parts of the answer from the reference link(s), as the answer can become invalid if the linked page(s) change. – DavidPostill Apr 22 at 11:21

The NTFS file system use a central "Master File Table" for storing the sectors where each files starts and which sectors belong to the file. This Master File Table is stored on the drive in form of an invisible file (MFT$).

It is crucial for the whole drive that this $MFT file has free space to store infors for new files, therefore Windows reserves some megabytes - this is most likely one part of the used space you see. Therefore event if you format a drive the now complete empty device will again have some used space because the $MFT file is there.

Furthermore there are other hidden files and folders, such as System Volume Information (contains the volume shadow copy files), pagefile.sys, hiberfil.sys and more.

For more details on the MFT see the Microsoft article "How NTFS reserves space for its Master File Table (MFT)"

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