If you need to run rebuild the folder structure on your drive on the internal startup drive of the Mac in Drive Genius 4, the drive needs to be unmounted. To unmount the internal boot drive, follow the steps below:
Create a BootWell™ drive using Drive Genius 4.
Make sure you have the drive backed up.
Restart your mac from Startup disk in System Preferences or use option boot.
In Drive Genius 4 choose your internal boot drive on the left then go to Rebuild.
If Rebuild is successful then you are done.
Quit Drive Genius 4 and do an Option boot. To boot back into your internal hard drive.