Cook the macaroni according to package directions. Drain and set aside.
Meanwhile, in a medium saucepan, melt the butter. Whisk in the flour for around one minute. Add in the milk, and whisk until fully combined. Bring the mixture to a boil, then reduce heat to a simmer, stirring frequently until thickened.
Add 2/3 cups of feta and the mozzarella cheese to the milk mixture, and cook over low heat until the mozzarella has melted. Season with the salt and pepper.
Pour the macaroni into the cheese sauce, and toss to coat. Mix in around 3/4 of the crumbled bacon.
Pour the mixture into a lightly greased casserole dish, then sprinkle the top with the remaining Feta cheese and bacon.
Set the oven to broil on high, and cook the macaroni for around 2-3 minutes.