Hi - thanks for replying.
Yes, the clipped view will be used with the make2d command and it should Make2D the clipped model.
There is plenty of software which does that, a few comes to my mind:
- rhino with the clipping plane command (http://vimeo.com/m/43613999): When you run the Make2d on a clipped view it will output the clipped model and not the whole model.
- sketchup with the Section Plane tool: it's a real time clipping tool and when you export as dxf it will output the clipped view.
- Fusion 360: Same thing goes here with the Section Analysis tool.

I hope I was helpful on your doubts.
Max.