Windows Defrag does a fairly decent job of keeping your drives defragmented and running smoothly. But sometimes, it has problems with large files. I usually run into problems with virtual machine drive images, once they get over about 2-3GB, they just don’t seem to defrag anymore.
Fortunately thanks to yet another Sysinternals tool called Contig, you can clean up those large files easily. Contig is a single-file defragmenter that uses the existing defrag API within Windows. After running it on a couple of my drive images, it took them from over 400 fragments each to less than 20. I did find it helpful to run a defrag pass on the drive before running contig on the large files.