Using Defrag software

Can anyone please tell me if I still need to Defragment my hard drive while I use Comodo CTM.

No, you shouldn’t.
If you need to do so, uninstall CTM (to the current snapshot), boot, defrag, install CTM again.
Using defrags while CTM is running is just increase the size of the snapshots and not really defragmenting the files (only what you “see” in Windows).

I am currently using a multi-boot system . Do I need to uninstall CTM from all the partitions to defragment the my hard drive ?

Is CTM installed in all operational systems?
Is CTM protecting all partitions/disks?

You can defragment partitions/disks NOT protected by CTM without problem.