Bring water to boil in pasta pot using amount per the pasta box
Add pasta and cook per the box instructions.
While that is cooking. In a saucepan, melt the butter over medium heat.
Once the butter has melted, add the flour to the pan and whisk continuously for about 2 minutes to cook off the raw flour taste. This creates a roux.
Gradually pour in the milk while whisking constantly to prevent lumps from forming. Continue whisking until the mixture thickens and comes to a simmer, about 5 minutes.
Reduce the heat to low and add the salt, black pepper, and ground nutmeg. Stir well to incorporate the spices into the sauce.
Add the grated sharp cheddar, Gruyère, and Fontina cheeses to the sauce. Stir continuously until the cheeses have melted and the sauce is smooth and creamy.
Once the sauce has reached the desired consistency and the cheeses have fully melted, remove the saucepan from the heat.