When you perform a headshot on an ant, their head will blow of, then you can quickly pick it up before it disappears. It is also possible to shot at the heads of the ants when they are already lying on the floor, it has the same effect. You do have to collect the heads to earn this achievement.
Edit: Gamer Taeglin pointed out, that you can use your shurikens to always decapitate the ants and you can also reuse these weapons.