MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I've made a version that uses spherical magnets here: https://www.thingiverse.com/thing:3596365

Also I exported my cork coaster piece so it's in the file if you want to experiment with an infill based coaster.

Tabletop Board Game Organizing Trays (Spherical Magnets)