Proteins and water. Clarified butter is made by melting regular butter at a low temperature. Three layers will form: the top frothy layer contains the proteins from milk (casein, used to make cheese); the middle layer is water with dissolved milk sugars, like lactose; the bottom layer is pure butterfat or milkfat, which is also known as clarified butter. You can instead heat butter at a low temperature for a long time to remove the water by evaporation, and then decant or filter the butterfat. Clarified butter contains almost no proteins, so it has a very long shelf life, and no lactose, so people who are lactose-intolerant can eat it.