Preheat oven to 350 F. Cook pasta according to package directions, drain. In a large saucepan over medium heat, melt butter.
Whisk in flour and cook for a minute to brown. Pour in milk and cheese and season with salt and pepper. Continue to cook over medium heat, whisking constantly until the cheese sauce has thickened and is smooth.
Mix the sauce with the cooked pasta. Cut the tops off of the bell peppers and remove the seeds. Fill each pepper with the mac and cheese. Place onto a large baking sheet and sprinkle each pepper with shredded cheddar cheese. Bake for 20-25 minutes.
