I want to make a tool similar to zerofree for linux. I want to do it by allocating a big file without zeroing it, look for nonzero blocks and rewrite them.
With admin privileges it is possible, uTorrent can do this: http://www.netcheif.com/Articles/uTorrent/html/AppendixA_02_12.html#diskio.no_zero , but it's closed source.
I am not sure this answers your question (need), but such a tool already exists. You might have a look at fsutil.exe Fsutil command line tool. This tool has a huge potential to discover the internal structures of NTFS files and can also create file of any size (without the need to zeroing it manually). Hope that helps.
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