Due to chronic UTI's I have had several cystoscopys. While they are no fun, they are not excruciating either. The doctor (or his nurse) will put a numbing gel in your urethra and let it sit for about 15 minutes. This will anesthesize (deaden) your urethra, making passage of the scope easier. Generally a flexible scope is used, which is much more tolerable. I have had both rigid and flexible.
The test takes only a few minutes, no more than 10-15, including time for tissue samples if needed.
If you are really nervous, sometimes it can be done in the hospital with sedation. This way you won't be aware of what is happening.
If you have blood in your urine, it needs to be evaluated. Hang in there, it's really not that bad!
Here's a link for more information:
http://www.webmd.com/a-to-z-guides/cystoscopy-16692