If you’re using a more robust defragmentation solution like Defraggler or MyDefrag, you might notice that when you’re done, there are still a couple of large files that didn’t get defragmented. Typically these are larger files, greater than 50 MB or so, and it happens quite frequently on removable USB drives.
The trick to defragmenting these files is actually quite simple: Just move the file(s) off the drive you’re trying to defragment, then defragment the drive. Once it finishes, move the file back to the drive and defragment it again. Nine times out of ten, this will do the trick.
If it doesn’t work, it’s generally because either you’re running low on space, so it has to store the file any way it can, or the file is entirely too huge to be in one fragment. These are usually files greater than 1 GB.