Melt it slowly.
You will get some white foam that rises to the top. This is part of the milk solids. Skim them off the top with a spoon. You can keep the solids to spread on other stuff if you want, although I usually throw it away since I don't really eat bread or other stuff that I would be spreading mild solids on.
Once you get it skimmed, the butter will start to clarify (Ghee is sometimes called "clarified butter."). Keep cooking it on low/medium low to get it as clear as possible.
I also have a glass jar to keep the finished product in. You can use whatever you want, but I prefer glass. Once your ghee cools you can store it a room temperature. Actually, I suggest that you do exactly that so your ghee will be soft and easy to use.
Once your ghee is solid it will turn a pale, beautiful yellow that you will now forever associate with the flavors of good eatin'. It's now time to saute something.