Hi RJ, you can use the "untrim" operation to remove holes like that, some details here:
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
It's also covered in the object repair tutorial here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=446.17
So for your case here you would delete these unwanted faces:
Now select this edge:
And hit Delete, it will remove that trimming boundary so the underlying surface won't be trimmed there anymore:
The one on the underside is a little more complicated though, you need to select this face and use Edit > Separate to break it off into its own individual surface not joined to the main piece anymore:
Then the part that is more complex is that this hole goes through the "seam edge" of the closed surface, so the full trimming boundary that it is a part of includes all these edges. To select them select one edge on that detached surface and then do Ctrl+A (SelectAll):
Currently to do an untrim you have to have the entire loop making up the full trim boundary selected, you can't have only some edges of the loop selected. That's something I would like to tune up in the future.
But for now when you then hit delete, the whole original surface will be recovered:
Then you'll need to retrim it to cut off the excess outside. The quick way to do this is to select it, run Edit > Trim, then push Edit > Hide to hide it and get it out of the way for the moment, then run the "Select naked edges" script set up on the N shortcut key as described here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=6051.2 , that will then get the fillet edges selected as the cutting objects. Right click to accept that, then pick the 2 outer pieces to remove, right click to end that stage and then you'll have this surface which can be joined in with the main piece using Edit > Join:
- Michael