Booleans create alot of issues down the track, especially when trying to get rid of holes. Avoid them if you can, instead of booleans in blender, use the following key combo
get your object, press tab go into Edit mode
press in the following order
K
Z
C
This will allow you do cut through your object like a knife which will create a vertice line you can cut manually and then deal with the edge loops yourself and not hope netfab will do a magic job (which it doesn't.. alot!)
Make your cut and press space bar to apply it, your dots will go red indicating you made the cut.
If you want a free cut, just press K and Z and omit C so you don't have the angle constraint.
Feel free to message me, I'd prefer to let this thread die as the OP hasn't logged on since he posted it 8 days ago, obviously wasn't very important to him but I don't mind helping you out with Blender, has a small learning curve but the best for modelling freely without the mess of autodesk and other cad programs. Does metrics very very well so you can model to precise scale.