How can I top/trim after flowering starts

My plants are in an enclosed box with a limited height. They are in the 2-3 week of flowering and it seems like they will eventually get tall enough to be touching the lights (CFL's). I can't raise the lights anymore and am worried about what will happen if they grow into the lights. I heard you shouldn't do any cutting during flowering, so is there any way that someone can tell me to keep them short or to trim them once they begin to flower? Will I just have to cut off the top buds, or the tops of the top buds? Or should I just let them grow into the lights and let the part that grows into the light burn and stop growing, allowing the plant to focus its energy in other parts.

you don't want to top them, too late. you could tie them down or throw a screen in there and do a scrog.