This achievement will come over time as you play through the game. Anything that attacks you counts as an enemy. To see your total amount of kills so far, visit your inventory, and use the Book-o-Stats. If you somehow did not get 3000 by the time the game is over, just revisit areas since enemies respawn after a while. You might get this achievement before or after you reach 3000 kills. I've seen people on the leaderboard that have only 2500 kills and already have the achievement, while I myself didn't get the achievement until about 3100 kills. Just keep at it until it unlocks.