Sift the flour and salt and pepper together in a large bowl. Beat the eggs and milk in a medium bowl. Alternately mix the milk mixture into the flour until a smooth dough is formed.
Bring a large pot of salted water to a boil over medium heat Press batter thorough a spaetzle maker into the water. When the spaetzle float to the top of the water, remove them with a slotted spoon to an oven safe dish. After first layer of spaetzle, add a layer of Swiss cheese. Continue layering until all of the spaetzle and cheese have been used.
Bake the spaetzle until the cheese is melted, about 30 minutes.