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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I'm sorry to hear that you have issues with my design. However, as the holes of the case and cover are the same in tinkercad, they should align. If they are off by only a little bit, just take a drill and widen them on the cover. If they get too wide, use washers with the screws.
I also had a similar problem once, and to fix it, print a 20x20x20mm cube and measure the real lengths. You can adjust the steps per mm in the firmware.