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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The bottom should not be popping off. Also by adding the top part this shouldn't be happening.
Except for one screw on each side the rest is optional. The holes are closed for esthetics, cleaner print results. You can easily remove the first layer by using a small sharp knife.