Hi,
if you are convinced you need a flat surface then use the rectangular pocketing Wizard that ships with Mach3. It will generate Gcode
to cut a pocket, the base of which will be flat.
I would not recommend holding the PCB blank down with clamps or screws around the periphery, it distorts the blank and all that effort you put into getting a flat surface
to work from is in vain. I would use double sided tape. Note also that fiberglass PCB blank board almost always has some warp or bow in it, usually not more than 10 thou
over several inches but its enough to cause problems when isolation routing. Double sided tape can help pull that bow/warp out of the board.
With Autoleveller I don't bother machining the spoil board flat, the probing and subsequent Z axis Gcode optimization obviates the need for it.
Craig