Preheat the oven to 200°C.
Cook the macaroni pasta according to the package instructions, drain and set aside.
In a large saucepan, melt the butter over medium heat. Add the chopped onion and sauté until soft and translucent.
Add the flour and stir for 2-3 minutes to create a roux.
Gradually pour in the milk, stirring constantly to avoid any lumps forming.
Bring the mixture to a simmer and continue to stir until it thickens.
Add the shredded cheddar cheese and Emmental cheese to the saucepan, stirring until the cheese has melted and the sauce is smooth.
Season with salt and black pepper to taste.
Add the cooked macaroni to the sauce and stir to coat the pasta evenly.
Pour the Makaronilaatikko mixture into a 9x13 inch baking dish.
Bake in the oven for 20-25 minutes until golden and bubbly.
Serve hot.