What most people do, is, in Cut 2D, set the top of your part to Z=0, and zero the Z axis to the top of your part.
There is another way. In the Homing/Limits screen, set the Home Offset for the Z axis to 4. That way, the table will be at Z=0 and the home position will be Z=4. Then, in Cut 2D, set Z=0 to the bottom of your part. The problem with this method is that if your part thickness is not exactly what it's supposed to be, your cut depths will be off by that same amount.