Resetting Old Machine


Hi there
I have recently upgraded my setup and I want to format my old machine and make a clean install. The machine has three drives and I plan backing up the system drive on one of the other two drives.
How do I do that....when I engage Time Machine it says that the backup takes up 1.49 TB but the actual content of the system drive is only 250 GB. I assume it's because it backs up all 3 drives.
Is there a way to make it just back up the system drive. Actually I don't care about the system, it's more that I want to be sure that I get everything apart from that which I will copy back into the right folders after the install.

All the best