Preheat oven to 375F. Grease a 13 x 9-inch baking pan.
Cook pasta in salted water according to package directions. Drain.
Melt butter in saucepan over medium heat until foamy. Whisk in flour and cook 2 minutes. Slowly whisk in milk, making sure there are no lumps. Add pumpkin puree and mix well. Remove from heat. Add cheeses, salt, nutmeg and black pepper
When cheese is melted combine with drained noodles. Pour into baking pan.
Bake uncovered 25 to 30 minutes or until golden and bubbly.