There could be a few reasons that the files are not visible. The first reason is the most obvious - they are not visible. I know, I know, that's the problem. It could also be the solution. If the files are hidden, meaning they are given the attribute *hidden*, they cannot be viewed unless you select view hidden folders. In windows 7/8 click anywhere in the window you are trying to view. Press alt. A menu bar should appear at the top. Select tools. Select Folder Options. You should have 3 "categories" available near the top of the new window that just opened. Select View. You should see a new, scrollable box appear in the middle of this window. Inside that box there should be a radial button with the description "Show hidden files and folders". Select that radial button. Hit ok. Voila, if they were hidden, they are now visible.
I know, that's too easy, and probably not the cause. Always better to get the simple out of the way first before getting complicated ^.^
Next is another easy one - Are you looking at the right user profile? There will probably be several. You should see Default, Administrator and your profile, to say the least. There might be more. Ensure that you are in the correct user folder.
Now, no, I didn't ignore that you are in DOS doing this. The reason I went on that GUI based tyrade is due to the simplest solution being present here. Use an OS to do the backup. It doesn't matter which. The easiest way is to take your HDD to another computer and plug it in as a slave (meaning not primary, not the master drive that is being booted off of. Back of the drive has the jumper to change this, BIOS has the settings to affirm it). The second easiest way is to make a bootable CD using a friends PC and use that. Linux is free. And small. (Some of them, anyway). The third way is to use Windows itself on your PC. Go to install drivers during install, or through any screen you CAN access, assuming it gives you the option to load drivers. Or read a readme. Or do anything that gives you access to a file browser. Using this file browser, you should be able to copy (not move, it probably won't let you do that one) files from one location to another, assuming of course that they are not encrypted or read/write protected.
The final method I can think of is in all reality the easiest. Just copy everything. Hidden files get skipped sadly. Use Xcopy c:/users/ Z: (Z being the destination of your choice). That'll just copy everything right on over for you to sort through at your convenience. Once again, assuming that it allows you to access it.
Hope this helps.