For an actual fit, you can't really do it yourself without extended riding and testing, usually with a powermeter or other method to measure performance, and someone willing to take video and still shots of you on your bike.
What a fitter should be doing is measuring your body morphology (shape and structure), and then using that to get you into a correct sized frame (whether it's road, mountain, time trial, etc), and then adjusting the fit using different length stems, handlebar widths, seat posts/seats, etc. to get the bike comfortable.
There are several different methods, including Fit Institute Slow Twitch (FIST, usually used for time trial/triathlon frames), GURU, Retul, eyeball and a few others. Many of these use fit bike mechanisms where the "frame" that you are sitting on can be lengthened, shortened, raised/lowered, etc. Some (Such as the Retul) also have cameras that can pick out and measure all the different lengths and angles and provide a printout.
A fit, however, is only as good as the person doing it. There are good and bad fitters, and if you really want a good fit, I would do some research on the local fitters and their experience/certifications and word of mouth reputation.
A "good" fitting will probably cost between $150 - $500 US dollars, depending on the type of fit, follow up sessions, and number of bikes being fitted.
Part of the reason for the variance is that frame manufacturers (Especially in time trial/triathlon frames) do not really follow a "standard" measuring convention, and a 54cm top tube bike from Trek may fit very differently than a 54cm top tube bike from Specialized. Also, someone that is 5'10" with a 34" inseam will fit a bike very differently from someone that is 5'10" with a 30" inseam.
If all the guy does is have you stand over the top tube and say "Yeah, that'll fit ya", I would definitely seek a different shop.