Prepare macaroni as directed on box, except under cook slightly; drain.
While pasta is cooking, melt butter over medium low heat. Add flour and salt and pepper (to taste) to melted butter and cooked for approximately 5 mins., stirring occasionally. Slowly add milk to the flour and butter mixture. Cook until mixture starts thickening, whisking to keep smooth. Remove from heat and stir in cheeses. Stir until melted. Mix in macaroni. Pour the mixture into a sprayed 9x9 baking pan.