Preheat oven to 350 degrees F (175 degrees C). Grease an 8x8 inch baking dish.
Bring a large pot of lightly salted water to a boil. Add macaroni and cook for 8 to 10 minutes or until al dente; drain.
In a large saucepan, melt butter over medium heat. Stir in flour, salt and pepper until smooth. Gradually stir in milk. Cook, stirring constantly, until mixture is thickened and bubbly. Remove from heat and stir in 1 1/2 cups of cheese until melted.
In the prepared baking dish, layer the macaroni and cheese sauce.
Sprinkle with remaining cheese.
Bake for 25 minutes in the preheated oven, or until cheese is melted and lightly browned.