Bring a small pot of lightly salted water to a boil over high heat.
While the water heats, shred the cheddar and measure the butter, flour, and milk.
Cook the macaroni according to the package directions until al dente, then drain in a colander and set aside.
In a small saucepan over medium heat, melt the butter. Whisk in the flour and cook, whisking constantly, until it forms a thick paste and turns lightly golden, about 30 seconds to 1 minute.
Slowly whisk in the milk, breaking up any lumps, and continue whisking until the mixture thickens and begins to bubble at the edges, about 2 to 5 minutes.
Remove the saucepan from the heat and stir in the shredded cheddar until fully melted. Season with salt and pepper, and add a pinch of cayenne and/or nutmeg if using, to taste.
Toss the drained pasta with the cheese sauce until evenly coated. Serve immediately.