For your fillet case, unfortunately that's a lot more difficult kind of fillet than what you may initially think.

The problem is putting in fillets cuts away some areas of the object and would cause holes to open up, filling in the hole for this case is not handled well by MoI's current fillet engine:








Above I used Edit > Separate to break those 2 surfaces away from the main object, then with them as individual surfaces instead of joined together Fillet operates in a different mode called surface/surface fillet, it is able to generate fillet surfaces in situations where the edge based filleter can get confused. So it is possible to make some progress on getting those fillets done that way but you would need to do some manual work on figuring out how to deal with that hole area.

I'd recommend trying that kind of fillet case in another CAD program that has a more sophisticated fillet engine that handles more types of junctures, try OnShape or ViaCAD.

- Michael