I would recommend a hobby knife and a very fine file or sanding stick to smooth the nubs on the window frame. Then, as mentioned above, cut a piece of strip styrene plastic (with matching cross section) to the height of the opening. Cut a second thin strip - longer than the opening - and (styrene) cement it to the first strip. Paint with acrylics, then cement the two assembled strips to the model from the inside. Use cement only on the two ends of the longer strip where they contact the inner surface of the wall. That way, no cement will mar the visible surface of the model and the mounting will be solid. I don't think a slight difference in color will be important as long as the repair looks to have been done carefully.
MELGAR
