Most likely you have some files that are in use while defragmenting that can not be moved. First try and using task manager to end every task you can. If you get almost everything closed, you should be able to defragment pretty much everything.
That should get it, also a third party defragmenter that can run before windows starts up may also help too. I have used O&O Defragmenter in the past, and it works pretty good. Not sure that it is worth paying for, as the Windows defragmenter works well.
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