Cook the macaroni in boiling water for about 10 minutes until tender but still firm. Drain well and set aside.
In a deep skillet, melt the butter over medium heat. Add the flour to make a roux and cook, stirring, to remove any lumps. Pour in the milk and cook until the mixture is thick and smooth. Season with salt and pepper. Stir in 2 cups Cheddar and continue to cook until melted. Add the cooked macaroni and stir. Transfer the mixture to a 2-quart casserole dish. Bake in a preheated 350-degree F oven for 20 minutes. Remove the casserole from oven, top with remaining 1/2-cup cheese. Bake for an additional 5 minutes until hot and bubbly.
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