I think that you should write a letter to the medical schools explaining the situation. In addition, it is a good idea to be affiliated with a church, or depending of you religion, some sort of a religious institution. Medical schools generally assume that the church people would not lie, so for example, if you are not talking to your mother/father, and you have not had any contact with them for years, the priest from the church, who knows you, can write a short letter to the school stating that you have not had any contact with your family for a number of years. I think it also works if a police officer, or another state person can write such a letter for you. Check out with the financial aid office, and see what the deal is, usually they have a section of things you need to do to prove that you are completely separated from your parents, and have no contact with them for a very long time.
I think they are pretty accomodating, that's why you have to file the application, each of us have unique circumstances.