My background is that I used to work part-time as a physician at a MEPS (Military Entrance Processing Station) in the US.
There can be some variety depending on the gender of the examiner. Let me tell you how it goes when there is a male examining females. All the females go into the female-only area and sit and wait. Usually they do the urine drug testing first. I (as the physician) have no part in this. The girls go into an attached bathroom (I don't see or hear what goes on in there). They pee in a bottle while a staff member watches them. Then they come back in to the female only waiting area.
I'll call the females into my exam room one at a time. I'll go over their medical history in a very detailed way. They have all filled out a DD-2807-2 (https://www.esd.whs.mil/Portals/54/Documents/DD/forms/dd/dd2807-2.pdf) before they come in, and I go over their answers and ask some other questions. The amount of time depends on how much history they have. I then do a physical exam from the shoulders up. All of this happens with the female applicant fully dressed. We are alone in the exam room with the door closed. I always tell them right from the beginning that I am only going to examine from their shoulders up during this part, and they won't be getting undressed, and that I'm closing the door for their privacy.
After I go over everyone's history and the exam from the shoulders up, the female staff member in the room has everyone strip to bra and panties. The girls come back into my room, this time with the female technician as chaperone. I do the rest of the physical with the patient in her bra and panties. After everything is done, the female goes behind a screen in my exam room, takes off her bra and panties and puts on an exam gown. She comes back out and sits on the exam table. I have her lower the gown and I do a visual breast exam, without touching. If she has pendulous breasts, I'll ask her to pick them up so I can see the underside. Then she puts the gown back up and lays back. Her feet go in the stirrups. I do a brief exam of her vaginal area, including spreading her labia majora to check the mucus membranes inside. There is no internal vaginal exam. Other than spreading her lips open, I don't touch or palpate any other part. Unless I see anything weird, the exam probably takes 5 - 10 seconds. I then have her stand up and bend over the exam table to take a 5 second look at her anus and butt.
Bottom line - it may make for a great fantasy, but in the real world, it is not exciting at all. I'm pretty quick and professional. I have a very experienced female staff person in the room and I am pretty confident that anything inappropriate on my part would be noticed.