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.
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