You get pulled aside while the agent manning the scanner yells for a "male/female assist" (depending on your sex). It takes somewhere between 30 seconds and 30 minutes for them to find someone to grope you.
You're then taken around the scanner, asked to identify (but not touch) your luggage. They pick up your luggage, lead you over to a screening area (which is in public view; they give you the option of a private patdown. I always elect for the public one, as I want people to see and question what's going on), explain their procedure, have you pose as though you're being crucified, and give you a very thorough groping which includes putting their fingers into your waistband and feeling your junk and buttocks with the backs of their hands. They then swab your luggage and their gloves (with which they have just groped you) and put it in an explosives detector. If the machine doesn't find anything, you're free to go. If it does, you're pulled into a small room and given an even more thorough search. The last time I flew out of LGA, I was subjected to this secondary search; the agent said it was probably alerting on the sunscreen I'd put on the day before.
The second search came up clean, but I was extremely amused to find that the room they searched me in was the room in which they kept their 5-gallon buckets of confiscated cigarette lighters. I was left alone in this room - with my luggage, past the security checkpoint - while the agent ran his second explosives test. I didn't do anything untoward, but man, if I was a bad guy it would have been trivial to stuff my bags with a bunch of containers holding flammable liquids.
I don't get hassled all that much when I opt out, but I'm also extremely white. I imagine that would be very different if I were brown and/or had a foreign accent.