1. Free up space before running Defragmenter. Clean out the recycle bin and use Disk Cleanup or download
CrapCleaner and use that to your advantage.
2. Run Defrag in safe mode overnight to reduce # of services running
3. If you still have problems, type this into the command prompt:
When it asks to schedule on reboot, press Y and then reboot and allow the disk to be checked. This exercise will probably take an overnight run.