The MFT is the single most critical file on any volume since it is a record of all the files on the volume. Don't manually change it in any way; Windows manages it's size automatically.
The windows defragger or the freeware defraggers cannot defrag the MFT to the best of my knowledge. You'll need a commercial defragger; google around, there are free trial versions available. Infact, the commercial defragger I use is fully automatic and defrags the MFT even within Windows (no need for boot-defrag) during the auto defrag.
If the MFT is fragmented into just 3-4 pieces it's not a cause for concern, but heavy fragmentation of the MFT can lead to slower disk performance since the MFT is accessed each time a file is read/written.