Although this is not am advertising site, I'm using Diskeeper for a long time, it is a program running as a service and defragmenting your disks on the flight keeping them defragmented. On formatting the disk you can set clustersize and it is wise to use 4k on a disk above 250 Gb or your $MFT will go heavily fragmented. Diskeeper has an option to defragment and even resize $MFT at boottime, as far as I know the only program able to do so. It is not free, but its money more than worth.
Diskeeper is spelled right with one k