After you beat the game, enemy spawns are massively reduced. Make sure all of your Board Countermeasures are for the Executive or Research areas, and try to get countermeasures that require few kills. To cycle your countermeasures simply take the ones you don't want and abandon them, and another one will be available. Also make sure to have all assist settings enabled to make it faster. To complete this achievement you will want to go between the "Central Research" and "Mail Room" checkpoints. For Mail Room, take the bloody door to the left of the checkpoint and that room will have enemies. For Central Research jump to the bottom of the stairs and walk back up and enemies should spawn. After you kill all enemies in both control points, quit to menu and start the game again. This is the fastest way I could do it.