Hi,
I am having a similar problem. Each time I subtract (tried different plug-ins as well) my main object is damage and prevent further subtractions. Anyone has a trick of how to subtract a grid of cylinders on a cube? I am trying to produce roundish pyramids.
Here are the files:
https://dl.dropboxusercontent.com/u/2637056/half-pipe-pattern2.skp
Thank you in advance!