It is a little uncomfortable but not really anything that big. I have had several done. Ask for them to put a little lidocaine gel into your urethra (they use a syringe without a needle and push it up from the opening of your penis. After a few minutes, you are numb.) for comfort. I just had a urodynamic study done and that involved a great deal more. Still, it was not that bad at all.
They don't actually use a catheter to say. It is a flexible scope which is like a small catheter that it attached to a monitor so that they can see your urethra, prostate and bladder.