How not to mill top surface?

With free machining and an stl file, I can’t figure out how to get EstlCAM not to mill the top surface. My part has mostly a flat top with some rounded pockets, and whatever EstlCAM settings I put in, it seems to generate gcode that moves about the top surface, quite pointlessly.

The simplest test was just to load an stl of a rectangular prism. I tried positive margins, zero margins, negative margins, Rectangular workspace, Shape as workspace, Custom masked, and lots of combinations, and they all insist of milling the top surface.

Am I missing something obvious?

A 3D file is milled that way can you export a DFX of the pocket and cut it as 2D?

No, the pockets have 3D profiles.

I wrote a little python script that removes the Z=0 moves from the gcode: https://github.com/arpruss/miscellaneous-scad/blob/master/scripts/gcodezerokill.py

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