MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.

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Awesome.. I just uploaded a step file of the Blank Stencil for you to play with.

You can import that right into Onshape (use the little plus sign in the lower left corner to do that) and then you can just draw what ever shapes you want on the top plane and extrude it upwards (with the remove feature) and when your done just export it as a stl (right click on the tab name at the bottom, select export, and then stl format) and its ready to print.

Enjoy.. let me know if/how everything works out.