Melt butter in a heavy saucepan over low heat. Whisk in flour gradually until smooth and all lumps are gone. Cook, whisking constantly, for 1 minute. Gradually whisk in 2 cups milk and cook over medium heat, whisking constantly, until mixture has thickened and is bubbly, about 5 minutes. Add Swiss cheese, salt, and pepper. Cook and stir until cheese has melted.