In a medium saucepan, over medium heat melt butter or margarine. Whisk flour and stir vigorously. Add milk and cook until thick and bubbly, about 5-7 minutes.
Add cheeses and stir until completely melted.
In a large bowl mix together the drained pasta and cheese sauce mixture. Toss to coat evenly.
Pour into a greased 2-quart casserole dish and cover. Bake in a preheated 350°F oven for 30 minutes.
Let stand 10 minutes before serving.