What is the best way to deal with intrusive medical exams and procedures when you are dealing with issues from abuse?

Well, if your abuse was from someone of the opposite sex, you should probably consider going to a doctor who is the same sex (that is, if you're a woman, go to a woman gynecologist). You should also tell the doctor about your past experience (you don't need to go into detail) and you should also insist that a nurse (or even a friend, if that's okay) be in the room with you. They don't need to observe. They just need to be there.