If it’s the one where they feed a wire camera down through the eye of your penis then yes I’ve had that done a couple of times. I was being checked for bladder infection due to blood in my urine.
In my case, they asked me to wear a gown with a square Velcro opening for your willy, which seems rather pointless as that’s the only bit that I consider myself naked.

Make sure you have a piss before the Cystoscopy. Once you are laid on the hospital bed, an anaesthetic gel is put on the end of your penis to numb it. The surgeon will then slowly feed a thin wire camera through the penis opening and do whatever he needs to do.
The bit you probably want to know is, is it uncomfortable? In my experiences, having the procedure done was not painful in any way, just mildly uncomfortable, especially when he fed the cord back out. It just made me recoil slightly.

Things that I wasn’t comfortable with:
How close his head got to my penis when he was looking through the end of the camera as he fed it in.

After the Cystoscopy is over, the anaesthetic gel will still be numbing your bits, so you won’t know if you need a piss or not.

When you do go for a piss, be prepared to piss flames. That bit is really uncomfortable, and you’ll continue to piss flames for the rest of the day.