Iaijutsu Focua allows bonus d6's in damage (up to 9d6 in the 50+ range) based on what your modified roll is. It also acts as your initiative roll in Iaijutsu duels. In non-Iaijutsu duels it acts as bonus damage for all of your attacks versus flat-footed opponents, but you roll initiative normally. In a duel it only counts on your first strike, successful or not.
My Samurai is now a 10th level Iaijutsu master/6th level Samurai. He'll probably kill most enemies in his initial attacks, even characters monster the same level he is. In just my lst game I played him in I fought a 17th level barbarian. I killed him before he could swing, all because of my Iaijutsu focus/mastery. And crits/keen blade/high strength, and I rolled well enough to get an extra 7d6 Iaijutsu damage per attack, plus he was flat footed for all of my attacks, so they all hit. He had around 222 hit points.