Is there a problem in putting an oven over the microwave oven?
Do you still have the microwave manual? In there it should give the minimum clearances for the oven. These will be required to allow for sufficient airflow around the microwave so that it doesn't overheat.

If it's 3 cm or less (which is unlikely) then you'll be OK.

For the more likely case of it being more than 3 cm, why don't you build a shelf at the right height above the microwave and sit the oven on that?