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.
That doesn't sound good at all... the design is not like this and they have printed well for me (on my MakerBot's) and plenty of other members here on Thingiverse without this sort of issue... no sanding/clean up required. On this basis it has to be something to do with the slicer settings and /or machines accuracy/precision on the lower layers. In addition, are you using a raft... this is recommended as it can leave the base edges cleaner (...but not all slicing apps / machines create as good raft with easy separation as others).
This is all I can suggest to help but hopefully you have everything sliding smoothly now albeit after some sanding.