Preheat oven to 350°. In medium saucepan, slowly add 1 cup milk to flour, stirring constantly until all lumps have dissolved. Add remaining milk, stirring thoroughly. Place on stove and simmer 15 minutes, stirring occasionally until sauce thickens. Add 1 cup Cheddar and all the Mozzarella and Parmesan cheese; stir until blended. Add macaroni, stirring gently to coat well. Line muffin tin with paper muffin cups and place one scoop of mac and cheese mixture into each muffin cup. Top with reserved 1/2 cup shredded Cheddar. Bake 15 minutes or until golden brown. Let cool 5 minutes before serving.