My MFT is 99% filled and fragmented into 2 pieces How to defragment it ?

Use Contig.exe which is a program in the SysInternals Suite. You do not need to download the entire suite. You can download only Contig.exe. http://technet.microsoft.com/en-us/sysinternals/bb897428 The first time you run defrag will take much more time than the second time. I recommend running with the -q and -s options.

The MFT will fragment when it gets too filled up (at 99% of capacity, it's surprising it only fragmented into 2 pieces -- you should handle it asap before it fragments more). I suggest you download Diskeeper to defrag the MFT (you can get a 30 day free trial at http://www.diskeeper.com). Once installed, you can have it examine the MFT (as well as any other system files you want) and it will compute and recommend an appropriate size that will keep it from fragmenting in the future. Once it has done this, go ahead and ask it to perform the suggested action and it will "pad" your MFT (increase it's size) and also defrag it (it may have to restart your PC to complete the task). Once complete, set it for automatic defrag (I think it's the default setting) and enjoy it for the next 30 days (the newest edition also prevents most fragmentation so it is a complete solution). After the trial you can decide to keep it or uninstall it -- it is a fully functional trial.

The MFT will fragment when it gets too filled up (at 99% of capacity, it's surprising it only fragmented into 2 pieces -- you should handle it asap before it fragments more). I suggest you download Diskeeper to defrag the MFT (you can get a 30 day free trial at http://www.diskeeper.com). Once installed, you can have it examine the MFT (as well as any other system files you want) and it will compute and recommend an appropriate size that will keep it from fragmenting in the future. Once it has done this, go ahead and ask it to perform the suggested action and it will "pad" your MFT (increase it's size) and also defrag it (it may have to restart your PC to complete the task). Once complete, set it for automatic defrag (I think it's the default setting) and enjoy it for the next 30 days (the newest edition also prevents most fragmentation so it is a complete solution). After the trial you can decide to keep it or uninstall it -- it is a fully functional trial.