When the surface of the butter is covered with a frothy white foam, reduce the heat to a very low temperature. Simmer, uncovered and undisturbed, until the gelatinous protein solids have collected on the bottom of the pan, and a thin layer of pale golden, crusty solids has formed on the surface. The cooking time will be about three hours. With a wiremeshed skimmer, skim off the thin crust on the surface. The ideal finished ghee is crystal clear and pale gold in color.
Ghee becomes dark when it is cooked on excessively high heat or is cooked too long.
Arrange a strainer, lined with three thicknesses of cheesecloth or one thickness of good quality paper towel over a large pan or bowl. Don't use paper towels with plastic reinforcing threads, as the plastic will melt. Ladle the clear ghee through the filter system to collect the protein solids from the ghee until you have ladled off as much clear ghee as you can without disturbing the milky solids on the bottom of the pan. These solids may be discarded. Be sure to cool the ghee to room temperature before covering.