Hi Bob, so to remove those holes the easiest method is the "untrim" process that Burr mentions above.

There are some examples here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=444.4
http://moi3d.com/forum/index.php?webtag=MOI&msg=9671.5

First select the inner "side wall" surface of a hole:



Delete that, there will now be open edges:



Select those edges:



Use Delete to remove the trimming boundaries that contains those edges:



- Michael