Preheat oven to 375. Butter four 1-cup souffle dishes. Dust with flour, and tap out excess.
Melt butter in a saucepan over medium heat. Sprinkle flour over top, and cook, whisking, for 1 1/2 minutes. Add milk, cheese, nutmeg, salt, and pepper. Cook, whisking, until thickened, about 3 minutes. Remove from heat. Whisk in yolks.
Beat egg whites until stiff peaks form. Gently fold cheese mixture into whites. Divide among souffle dishes, filling to 1 inch from top. Place on a baking sheet, and bake until puffed and golden, 12 to 15 minutes. Serve immediately.