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.
Thanks for your message and I hope I can help....
By a base layer I assume you mean a 'raft'.... different makes use different terms. Assuming so see if you can increase the raft / base to model spacing in your slicing app. On my MakerBots 0.27mm works really well. It almost always snaps away by hand. However, not all slicing apps or machines work the same or are as accurate / precise as others.
Take a look at the MakerBot website under their 'learn' tab. That provides a good introduction. Also visit their support tab thengo into the 'learn' section there as well. That area has some very informative content that applies to 3D printing in general, not just MakerBot. However you will need to search within specific model listings to find it.
Finally. .. try using a craft knife to slice away the base from your print. Refer to the images I included on Thingiverse.