There are several deframentation utilities that include a "boot time defrag" feature, which is the only way to defragment the MFT.
Perfect Disk: http://www.raxco.com/windows7defrag
Puran Defrag: http://www.thewindowsclub.com/how-to-defrag-mft-page-file-registry-system-files-in-windows-7
I also suggest you create a System Image using Windows 7 "Backup and Restoe" prior to performing this type of defragmentation for safeties sake.
J W Stuart: http://www.pagestart.com