As you heat and skim, the butter will further separate, and you will start to see milk solids start to fall to the bottom of the pan. Now is a good time to lower the heat and watch the butter carefully. You don't want to let the milk solids that fall to the bottom of the pan burn!
Continue to simmer the butter until you end up with a clear, yellow liquid with golden brown milk solids at the bottom. At this point you can strain the finished ghee into the containers you want to store them in. I usually just use a stainless steel strainer, but it's a good idea to strain the mixture with cheesecloth, especially if you have an intolerance to the milk proteins.
The transparent liquid that you obtain is your ghee. It will solidify as it cools. you can store it at room temperature for several weeks, or in the fridge for several months.