Super Duper question for first time user.

[weapon]

We had to do nuke and pave on one of our machines.

We loaded all of the software back in and then made a bootable backup copy in super duper and a separate removable drive.

We then added in the suspect software to the main boot drive. It continued to have the problem, so it was definitely the added software/hardware.

How do we go about erasing the main boot and replacing it with the clean version from the drive?