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 still have not figured out (I am new to 3D Printing) why there are "holes" in the print. It looks to me like there are one or two layers missing at the end to close them off.
Regarding the holes: Try more layers on top. You can use 5 or even 10 layers. You need more if you print with less layer height.
Check these tips
Also, check wether you have under-extrusion. This can happen if you didnt calibrate the extrusion. Check this