Do you mean modding the game so the enemies look different? I can't help you if that's the case. :p
Not modding, physically changing the files. For example, you copy your custom model, then paste it into the folder with the original file, like the MK 4 swordbot. Then, you delete the MK 4 swordbot model, and you have your own custom model for the MK 4 swordbot in your own game.