Thanks Michael for the reply. I don't have any duplicates. I need the inlay parts and the base that the inlay is cut into. So it's:

1. Draw 2D sketch on top surface of substrate
2. Extrude 2D sketch into substrate to create the inlay
3. Boolean diff to remove the inlay from the substrate.

Only after step three I no longer have overlapping parts.

Maybe the solution I need is a script that can take a 2D selection and perform the extrude and boolean diff in a single step. Then I would only need to select the 2D shapes.

Note that I get the overlapping surface dithering effect even if I only extrude the outer profile, so there is only one solid involved but the insides of the 2D sketches appear to be another surface.

Andy