When i look at Cut/Layers i see three options. Cut, Fill, and Offset Fill. Seems like i saw there was another option for putting lets say a box on the design that was just for measuring. Maybe i dont have that in my version. It was like trace or something.
Never Mind. I figured it out. To do what i want you have to use one of the T1 or T2 layers to make it a tool layer so it will not be part of the design