It is necesary to distinguish a real exam from a play one.
The real exam rules are done mainly by the general custom practice and partly by the doctor's habits, so the patient is usually minimum degree of undressing known. E.g. the patient is dressed when the doctor or nurse is taking his/her medical history. Then he/she is asked to strip to the underwear and scaling, measuring and main part of the exam follow.
If the doctor is to examine the breasts or genitalia, he/she ask the patient to remove the appropriate part of his/her underwear (if any gown is not used). Real examining in nude is not generally usual - except babies, soldiers, prisoners etc.
The play exam should be done under the scenario agreed by both the doctor and the patient.
So, for example, the patient is to be completely undressed after coming in the exam room etc. The play is one of the D/s relationships and the sexual arousing is usually the main reason for it.
Irrespective of the fact whether the exam is a real or a play one, you have to appreciate that the nude patient is more communicative and usualy reveals things he/she would not tell being dressed. That is one of the reasons why soldiers, prisoners etc. are usually examined in nude inclusive taking their medical history.