While the pasta cooks, melt butter in a large sauce pan over medium heat. In another sauce pot, heat milk (DO NOT BOIL). Add 3 tablespoons of flour. Cook the roux, stirring constantly, until thickened and nutty in color about 3 minutes. Pour in the hot milk and wisk constantly until thickened and the sauce coats the back of a spoon, about 5 minutes. Season lightly with salt, pepper and nutmeg. Stir in the cheeses a handful at a time and continue to stir until melted. Stir in the macaroni until evenly incorporated.