In a small saucepan, gently heat the milk without bringing it to a boil. In a separate large pot, melt 6 tablespoons of butter, stir in the flour, and cook on low heat for 2 minutes, whisking constantly.
Remove the pot from heat. Stir in the grated Gruyère, Cheddar, 1 tablespoon of salt, black pepper, and nutmeg until the cheese is melted. Add the drained macaroni to the cheese sauce and mix well.