While pasta is cooking, melt butter in a medium-size, heavy-bottomed saucepan (not nonstick) over medium heat. Stir in flour until well blended; cook 1 minute. Whisk in 1 cup of milk and cook, whisking continuously, until smooth. Whisk in remaining 1 cup milk and continue to cook, whisking until thickened and smooth, about 5 minutes. Remove from heat; stir in salt, pepper and nutmeg. Whisk in 2 cups of the cheese until smooth.
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