Yes.. the main stem, and any other branches that are gettin longer than you like. Wherever you top the plant it will bifurcate, and grow 2 more tops. I've seen deer eat plants down to just a main stem and the plant grew into a strong, bushy plant that yielded great. That's what you want ! Leave at least one growing point on each stem, so the new growth will take off quicker. New growers are hesitant to do this, but up until the middle of July, you can prune/top all you want.