Thanks..
But I have managed to do it using the default prune tool.
What I did is decreased the memory limit in php config and used 8GB memory using ini_set for thread.php file in admin cp.
Run the tool and waited for over 10 Hours.
Abhik, can you explain this in depth a little more? I need to delete 3/4 of my users, but when I try to delete more than a couple 10s of thousands my browser hangs.