01Preheat oven to 350 degrees F. Line regular muffin tin with muffin tin liners.
02In a medium saucepan, add 1 cup of milk to flour, whisking constantly to get out lumps. Add the remaining milk, stirring thoroughly. Turn on heat and bring to a simmer. Continue to simmer approximately 15 minutes, stirring occasionally, until sauce thickens.
03Add 1 cup cheddar, mozzarella, parmesan cheese, salt, pepper, and nutmeg; stir until blended. Add macaroni, mixing gently.
04Fill the 12 muffin cups with the macaroni mixture. Top each with remaining ½ cup cheddar. Bake approximately 20 minutes until golden brown. Cool 5-10 minutes before serving.