Ancestors will spawn after certain generators are started, and there will additionally be 3 more at the end of the level when defending the final area.
To get this achievement, make sure you pick up a hypno knife which will randomly spawn in one of the green crates. Now, once an ancestor spawns, use an overcharged shot from an NX-1 Disruptor to get the shields off, and then throw your hypno knife at the ancestor.
You will get a "hit-mark" an the ancestor but the hypno knife will be ineffective, although the trophy will unlock: