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.
It is not supposed to have holes. Standard settings with 0.4mm Nozzle should work. If you have your extrusion width (external perimeters) set much more that 0.45mm that might cause gaps at the walls between bricks. The wall thickness there is only meant to one perimeter thick. Also, if you scaled down the model at all that might cause the wall to get to thin to print.