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.
I'll try to upload them later.
The ability to make them is already in the code. There's a logo variable at the top.
I found a SVG logo and then loaded it into openscad (123D works too), and then extruded it 5 mm and saved as STL.
The code resizes whatever STL you give it to fill the tray.