Drop a bomb or other explosive device on the Na'vi. The RDA (Resources Development Administration) soldiers utilized this highly destructive tactic when they hit the Na'vi HomeTree with incendiary bombs. Many of the Na'vi were also crushed to death when HomeTree ultimately collapsed.
Kill the Na'vi with gunfire. The avatar of Norm, one of the scientists, was killed during the final battle scene of the movie. He can be seen being shot to death by enemy fire from the RDA troops. Grace Augustine, the leader of the avatar program, also mentions earlier in the movie that Neytiri's sister, along with other young Na'vi, were shot to death by machine guns after setting a bulldozer on fire.
Impale or otherwise stab the Na'vi. Neytiri's father Eytukan, the clan leader of the Omaticaya, died shortly after HomeTree fell. After fleeing into the forest and leading other Na'vi to safety, he was impaled through the heart by a large piece of wood, apparently from the explosion.