You just HAVE to run scandisk first, or your defrag will screw up your partition table if there are some invalid entries in there. That's what scandisk is for... fix errors before you really do some cleaning.
Do it right once, and you shouldn't have problems afterwards.
1. Run scandisk
2. Restart and let it go...
3. Close ALL the running applications (go in the task manager and look at proccesses that were started by your username. Leave the ones you don't know about but close all the rest. Don't touch the system ones of course)
4. Start defrag and LEAVE IT until it's DONE! It took about 3 hours for me once and it was only a 30 Gb HDD, so it can be long. But if you stop it manually, it's only gonna be worse when your system restart.
Defrag has to replace things in a good order, and to do that, it has to temporary move other stuff around. If you stop in the middle of that "temporary moving" the entries and gonna be even more messier than before. So you really need to let it go!