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I am having trouble with my Windows. I am considering options but before I do this I want to back my files up. In the past I booted into Ubuntu using a USB drive and copied files off the hard drive when I couldn't boot. I am attempting this now, hoever, I see some files but I do not see the folder that would be "My Documents" or contain the files on my desktop.

Is there a reason I am not seeing these files? Do I need to do something else to see all the files on the HD?

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No. If you can see some files on the hard drive but not others then it might indicate that there is a problem with the filesystem. Make sure that you change the view in Nautilus to show hidden files, but this is unlikely to be the problem.

You could try installing testdisk on Ubuntu on the USB and see if that can help you recovery the missing files. Check the partition and mount status of the NTFS partition(s) with the commands

sudo fdisk -l
blkid
mount

first so that you have a better idea what you are dealing with.

If you have an external drive that is big enough and has enough free space, you could make a bit copy of the internal drive and use testdisk to investigate the file system on it. This is SOP for data recovery, especially in cases where the drive may be damages or failing.

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BTW, I'd recommend that you thoroughly test that drive before installing any further operating systems on it. Also run an overnight test on the RAM. Frequent failure problems can be an indication of a much more serious hardware problem. –  fabricator4 Dec 22 '12 at 23:15
    
Thanks for the assistance. I have checked View Hidden Files but as you said that is not the problem. I do have a large enough external drive to make a copy of my drive to it to check the drive. The question is how? I am not very familiar with Ubuntu and would need step by step instructions. I can create another question if it would be better? –  Lynda Dec 22 '12 at 23:22
    
Hi, yes a separate question for that would be a good idea. AskUbuntu is more like a wiki format than a rambling forum. It takes some getting used to, but it works. –  fabricator4 Dec 25 '12 at 20:28
    
I was able to solve my issue that prompted this question, however, I am still curious as to how this is done. That question can be found here:askubuntu.com/q/232731/23251 –  Lynda Dec 25 '12 at 20:45
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