Yeap, my D: drive has 1,125,995 files, 34,597 folders. My MFT is over 1.4 GB in size and was in 5 fragments.
I did a normal defrag from the bat file I always use and when done my MFT fragments went back down to two. So defrag did work on the MFT. I did do a chkdsk before the drfrag though, the reason being with that large number of files it is very easy for the MFT and file system to not be correct and need fixed, sure enough chkdsk fixed a few things and I then did the defrag after.
The commands I use in my bat file are
start /wait %SYSTEMDRIVE%\Windows\System32\defrag.exe D: /H /V /U
start /wait %SYSTEMDRIVE%\Windows\System32\defrag.exe D: /H /V /X /U
Shane