Cook the macaroni according to packaging directions to the al dente stage. Drain and reserve.
Meanwhile, melt the butter in a medium saucepan, and whisk in the flour. Cook, whisking constantly, for 3 minutes until smooth.
Gradually stir in the milk and bring just to a boil while stirring continuously. Reduce the heat and simmer, whisking often until the sauce thickens slightly, about 4-5 minutes.
Add the salt, pepper and 2 cups of the cheese, stirring constantly until the cheese melts. Remove the pan from the heat and fold in the reserved pasta.
Pour the mixture into a prepared baking dish and top with the remaining cheese. Bake for 15-20 minutes or until the cheese is bubbly and the top is going to brown. Let stand for 5 minutes before serving.
