Not all files are defraged,this is nornal.

 

" So, after your defrag finishes, do you sometimes have a few files that refuse to defrag? If you do, don't worry too much about it. This is normal for most computers"

 

http://www.worldstart.com/tips/tips.php/3163

 

Regarding " mft"

 

" To prevent fragmentation of the MFT, NTFS reserves space for the MFT in an effort to keep it as contiguous as it grows. This is important because defraggers can not move MFT records and fragmentation of the MFT can severely impact performance."

 

http://www.jsifaq.com/SF/Tips/Tip.aspx?id=0487

The $MFT is the Master File Table, and a system file. It is analogous to a record of all the files and their attributes, on the disk. The windows defragmenter, and the free defrag utilities that you find on the net do not defrag this file. 

 

There are usually 2 MFT 'fragments' - one is the MFT itself and another is the 'mirror' of the first few crucial records in the MFT. The latter is stored in a separate area of the disk for safety. The MFT has some space preallocated to it, and does not normally fragment until the disk is beginning to get filled up with a lot of files.

 

To defragment the MFT, IF it has become fragmented, then you will need to go with a commerical defragmenter such as Diskeeper. That can defrag part of the mft during a normal defrag and the remainder during a boot-time defrag.

 

You can download 30 day free trial versions of DK here : www.diskeeper.com if you want to test it.

 

Hope this helps.