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I have had some success eliminating distracting things in the foreground of images by using the Z shift tool in the main window of MB3D.
Is the middle button on the bottom left of the screen, with the four arrows centered in it.
I used it by clicking on the button, then dragging down with the mouse on the image until the unit counter next to the button read 25, then I released the mouse button. I think this, in effect, pulls the image "closer" to you along the Z plane.
To see the results, you must render again.
By doing this repeatedly, I was able to finally get something out of the frame, and get a good image.
You might try that, and see if it will work for you.

I did this using cutting planes in this piece: http://cyanideclyde.deviantart.com/art/Escape-to-Infinity-372378015?q=gallery%3Acyanideclyde%2F43545516&qo=5

I didn't remove the obstructing cubes, but decreased their opacity. Reducing their opacity to zero eliminates them, though.

I cut the objects(2 cubes) out of the view in multiple cutting stages and then made a composite final image in Photoshop. It was a fair amount of work but should work for you, if you don't mind the extra labor overhead.