Heat oven to 350. Cook ground beef, onion and garlic in 10-inch nonstick skillet, stirring frequently, until beef is brown; drain. Stir in tomatoes, mushrooms, parsley, basil, fennel seed and salt; break up tomatoes. Heat to boiling; reduce heat. Cover and simmer 10 minutes. Spoon about 1/3 of the beef mixture into ungreased rectangular baking dish, 13x9x2 inches.

Mix cottage cheese, 1/3 cup Parmesan cheese, the nutmeg, pepper and spinach. Fill manicotti shells with spinach mixture; place shells on beef mixture in baking dish. Pour remaining beef mixture evenly over shells, covering shells completely. Sprinkle with 2 tablespoons Parmesan cheese. Cover and bake about 1 1/2 hours or until manicotti shells are tender.