(Originally written with the intent to gross people out. Then they started thinking with their dicks.)
 
"Ah! Wha- Anon! Not th- HNNG! Th-that's my butt! OW!"
>This is what your patient says as you stick two of your fingers into her anus.
>Looks like you skipped to the next part of the exam too quick without giving her time to let the information sink in.
"Sorry about that, Miss Sparkle. I had a feeling that maybe it would go better if I didn't give you time to worry."
>Maybe that wasn't the best thing to try to say to cover up your mistake, but whatever.
>She probably can't think straight with her rectum being stretched open by your digits, anyway.
>Twilight Sparkle.
>She came into the office today complaining about a stomach ache that had been persisting for an extended amount of time.
>You've never had her as a patient before, but her regular physician was out for the week.
>Turns out, you were the only one available at this time.
>The both of you are actually pretty good friends, you talked quite a bit with the bookworm when you first got here. Hell, you still get together with her a few times a week to talk and do whatever.
>Maybe she'll let your mistake slide.
>After realizing you've zoned out with your fingers inside your friend's butt, you continue with your duty of lubricating her up for the scope.
>That's one thing you found interesting about being a doctor here in Equestria.
>For some reason or other, most clinics only accepted you if you had at least one specialty in addition to being a standard physician.
>Let's just say that due to a lost bet, you ended up learning how to be a proctologist. 
>You feel as her sphincter tightens around your lubricated fingers while she shifts uncomfortably.
>"Nngh..."
>Twilight's face is contorted into that of discomfort, along with a heavy blush spreading across her cheeks.
>The ones on her face, you mean.
>You are starting to not be able to move your finger because of how tight she is getting.
>Fucking horse anatomy, man.
>With your free hand, you reach out and pat Twilight on the back.
"Hey, just relax; clenching only makes it harder for you and me. Try to push out instead, alright?"
>The purple mare reluctantly complies and relaxes herself enough for you to continue your job.
>"This is so... a-ah... embarrassing... and awkward..."
>The unicorn definitely has a point; you've never seen her in this kind of position before.
>For a few seconds, you rotate your finger around inside of her, being sure to lubricate her well for what is coming up.
>When you feel like you've gotten the flesh lubed up enough, you begin withdrawing your finger.
>As your digit slides out, she looks back at you, her brow scrunched up while biting her lower lip.
>You take off your specially made glove and toss it in the trash bin.
>Twilight watches you carefully as you prepare your tools.
>Looking over to her with the scope in your hand, you speak.
>"This is the proctoscope. I'll be using this to look inside of your colon to see if there is anything wrong.
>Twilight's eyes widen to the size of dinner plates, and she looks like she's on the verge of passing out.
>Yeah, you don't blame her.
>This isn't something you'd like to have done, either.
>Unfortunately though, all of the doctors here don't have fingers, and use scopes like this instead; or if they're unicorns, they have a spell to actually feel up there.
>That's one advantage that you have that the medical board somehow approved of in certain conditions.
>For example, lubrication. As opposed to introducing a lubricated scope all at once, you can start with your fingers first.
>Taking the bottle of lubricant, you squeeze a generous amount onto the end of the tool.
"Okay Twilight, I'm just going to move your tail back, and you'll feel me touching you back there. Then, I'll insert the scope."
>The pony nods, beads of sweat forming on her face.
>She stands up on the table, and turns so her backside is facing you.
>You step closer to her, and gently take her tail in your hand.
>Predictably, she tenses up at your touch.
>"Are you sure we have to do this, Anon?"
>You stop to respond.
"From what you said, you've been having problems for days. This could be serious, and you shouldn't wait any longer."
>The last thing you want to do is lose one of the few friends you have here.
>"I-I know... It's just that we're friends and all. It makes it worse than it already is..."
>You look up.
"I understand, Twilight. I know I can't make you do anything, and I'm not trying to be a pervert when I say that you shouldn't drop this appointment."
>A sigh is the response you get.
>"O-okay. You're right, continue..."
>Your hand returns to her tail, and you move it out of the way.
>Twilight's most intimate parts are exposed to you, and you would be lying if you said you didn't stare for a bit.
>There's always that feeling about seeing a friend of the opposite gender in a revealing position.
>On one hand, you've got pussy in front of you. On the other, there's a huge fucking elephant in the room for the next few days.
>Fuck it, you gotta focus on your work for now.
>While keeping her tail out of the way, you use your two fingers to spread her pucker.
>Yet again, she tenses up.
>Using the best calming voice you can, you speak.
"Just relax, I'll be gentle... Just do the same as you did with my finger, it will be just fine."
>You wait for her outer ring to relax.
>When it does, you carefully probe it with the scope.
>A small whimper is heard from her end as you start putting more pressure on.
>Soon, the tip of the obturator is all the way in, meaning all that's left is the thickest part, the scope itself. 
>"A-anon, I think it's t-too- Ngg! Too big..!"
>Okay, really. Sure, you wouldn't wanna go through this either, but goddam. You wouldn't be so afraid of it.
>You stop in an attempt to let her get used to the stretching.
>About a minute passes before she speaks.
>"I'm r-ready."
>No use in waiting around.
>You start putting pressure back on the proctoscope.
>The room is completely silent aside from the slimy sounds of the scope sliding into Twilight's poop chute, and her whimpers of discomfort.
>Eventually, the scope is in deep enough for you to look for any problems.
>You proceed by slowly removing the obturator, then set it aside.
>Before you start, you look back at her face.
>Twilight's eyes are clenched shut, tears nearly falling out of each one.
>Letting go of her tail, you place your hand on her back and begin to rub.
"You'll be fine. Now, could you raise your bottom in the air a bit more for me?"
>The blush on her face intensifies as she does what you ask with a groan of protest.
>The purple mare is now in a position so that her chin is touching the table, and she is using her front hooves to cover her face in shame.
>However, her ass is stuck way in the air, giving you a better view of everything.
>With that, you flip the built in light on and begin to inspect.
>Nothing too out of place here...
>Maybe just a bit of minor irritation, but nothing serious.
>"Twilight, when's the last time you had a bowel movement?"
>Her ears twitch when she hears your question.
>"W-what? Why?"
>You talk sternly.
"Just tell me, it will help."
>Through her lavender fur, you see the redness spread to her ears.
>"About t-three days ago..."
>Well, that would definitely explain some of her problems.
>That's really all you needed to know to fix this.
>Probably. Let it be known that you weren't quite at the top of your class in college.
>Seriously, who the fuck lets a lost bet determine their life's career?
>Okay, MAYBE you were still distraught with fear and anger about being ripped away from your world at the time.
>Oh well, no use dwelling, you're still on the job.
"Welp. I think I've found the problem. I'm just going to remove this, now."
>You replace the obturator, then start removing the scope. 
>While you do this, a sharp gasp followed by pained moans enter your ears.
>"A-aah! O-oooow!"
>This time, you just keep going, knowing that having it over sooner would be better than making her suffer.
>After a few seconds which probably felt like an eternity to Twilight, the scope comes out completely.
>You end up watching her slightly gaping butthole slowly close itself while she's not looking.
>Then, Twilight collapses to the table on her side.
>You internally chuckle, then reach into your drawer, retrieving two silo shaped pills.
>Today is just an anal probing kind of day, man.
"We're almost done, Twilight. I just need to give you some medication."
>You hold the two differently colored pills up.
>The poor mare looks traumatized as she realizes there is more to come.
>She sniffs, appearing to try to hold back tears, before she starts to get up.
"Actually, you're fine where you are."
>You take a step back to the examination table, and grab a new glove.
"I'll only use one finger for this, so it shouldn't be as bad."
>The bookworm pouts.
>"Whatever..."
>This has really taken a toll on her, hasn't it?
>Best to just do it quick.
>That's one good thing about being friends with a patient. They're less likely to report you for being unprofessional.
>You grab her tail again, and move it.
>Her anus is spread by your fingers, and you push the first suppository in.
>The unicorn grits her teeth and shuts her eyes as you do.
>"That one is for the irritation."
>How horses got something like that in this world, you'll never know.
>You pull out your finger, and ready the next pill, pressing it against her entrance.
"This one will help loosen the stool that's built up there."
>Hopefully it's not a blockage. To your best judgement though, signs don't point towards that.
>Your finger pushes it in.
>Once your hand is out, you remove the glove, yet again tossing it in the trash.
"That should do it! If you don't have a bowel movement within a day or two, or if you do and your stomach keeps hurting, come back ASAP."
>Twilight silently nods, looking near depleted of energy.
>Streaks from tears can still be seen on her face as you help her off the table.
>As you wash up your equipment, you look at her as she walks out of the office.
>She's sporting quite the odd walk now.
 
>A few days have passed since Twilight's visit to your office.
>Things have been... a bit awkward between you and her since then.
>You can't really blame her, she REALLY didn't like what you had to do her back there.
>Either way, at least she was okay now.
>You reflect on this as you finish up the internal exam of a female patient.
>That's another interesting thing about the medical system here.
>A "General" doctor pretty much means you're a urologist AND a gynecologist.
>No wonder med school here takes so damn long.
"Okay then, Miss Punch. Everything looks to be in order. You can check out at the desk down the hall."
>The magenta mare stumbles as she walks out of the door.
>"Yeah, thanks *hic* doc..."
>She's always an interesting one to work with, always showing up drunk.
>You sigh in exasperation.
>So many patients today, looks like this place is understaffed.
>Again.
"God dammit... why do I always end up drawing the short straw?"
>Someone your age shouldn't have to deal with this shit.
>You leave the room and look at your list.
>Next up is...
>Twilight Sparkle.
>You do a double take.
>Wait, what? Again?
>What the actual hell is going on here?
>You look over next to her name to see what she's here for.
>A full gynecological examination.
>The fuck? 
>Room 3A is where she is currently waiting.
>You are actually not looking forward to this.
>Many stallions in this town would kill to be in your position right now, but you...
>Your friendship with Twilight is already a bit strained as it is; what will this do to it?
>One of your co-workers walks by you.
>Could you maybe..?
>It's worth a shot.
"Hey, Dr. Stable, mind taking the next patient for me?"
>The yellow stallion looks at you with a deadpan expression.
>"We both know that can't happen."
>Your shoulders slump.
"Yeah..."
>There's no getting out of this one.
>You walk down the hall, towards the room where Twilight awaits.
>As you proceed, the question repeats in your mind.
>Why you, again?
>You walk down the hall with a mixture of emotions.
>Confusion, nervousness, arousal, and a hint of anger.
>Before you get to her door, you whisper to yourself with a bit of sarcasm.
"Eh, who needs friends anyway..."
>Your feet eventually stop at the door to the room that Twilight is waiting in.
>A few seconds are taken to steel yourself for what's to come.
>Raising your arm, you bring your fingers into a fist, and knock on the door.
>"O-oh... Come in!"
>Here we go...
>You grip the doorknob in your and and twist it.
>The latch comes undone, and you push the door open.
>Silence.
>An unsure Twilight sits on the examination table, kicking her hooves.
>It looks like she's doing her best to avoid eye contact.
>This is as good a cue as any to speak.
>You clear your throat, then begin speaking.
"Welcome back, Miss Sparkle. So, I see you're here for a..."
>You swallow.
>"A full... examination."
>She blushes and looks away.
>"...Y-yes..."
>Pulling up the closest chair, you sit down and face her.
"So, uh... Let's get started with some basic questions."
>...
>After getting some of Twilight's most personal information, you start the physical part of the exam.
>This part isn't so bad, just some innocent vitals, eye, ear, and limb checking.
>The whole time, she just sits there, staring off into space.
>Whenever you try making small talk, she just makes her answers as terse as she can.
>Eventually, you finish checking her back legs to see if they're fine.
>Next up are the more... awkward parts.
>These are the tests that are specifically for mares.
"Twilight, could you stand up and turn around for me?"
>The unicorn snaps out of her trance when you ask her this.
>"Huh? Already?"
>You nod.
"I haven't got that many answers out of you, are you /sure/ you want to do this? With me? I mean, it seems like-"
>She cuts you off before you can finish.
>"I need this done right away, Anon. I can't continue my studies if I don't get a check up..."
>You stare at her curiously.
"Aren't you the Princess's personal student? Is she making you get it this fast?"
>Twilight shakes her head.
>"I am, but I'm still a part of Celestia's School For Gifted Unicorns. They require a physical every year. The local mail mare lost the letter for a long time, and I didn't get it until I only had a few days left..."
>Fucking Derpy Ditz, whatever the fuck her name is.
>Looks like loopholes and weird rules exist here, too.
>Either way, that policy is fucking stupid, and whoever thought of it needs to get their brain checked.