Hi krass - that one in your post above doesn't work right because there is an extremely thin little sliver of an additional face in that spot, making a somewhat more complex edge structure in that area than you would initially think.

If you do some careful window selections (selection window drag from the left going towards the right so only things completely contained inside the window are selected), and delete the tiny thin sliver face then it should work better for you. I've attached a version where it should be ready to have the holes deleted now more easily.

If you need to remove a hole where the hole goes across several surfaces, it's a more difficult process to remove those, you typically need to do a broader untrim and then retrim after that. There is an object repair tutorial here which goes over the process: http://moi3d.com/forum/index.php?webtag=MOI&msg=446.17

- Michael