Right, pretty much like
@Pierman Walter said - just create three separate "enemies" and position them so that it looks like it's one entity.
The one bit of weirdness would be the fact that once you "defeat" a part, it will disappear, and you'll be left with two-thirds of an enemy. If you want that... great! You're done. Stop here. If you don't, you'll need to get a bit creative to solve that problem. Here's are two ways I might approach it:
1) Give every part, at the beginning of the battle, a state that resists KO. Have troop events that trigger when each part is reduced to 0% HP; these events should transform the appropriate part into a "Destroyed" version that has no Enemy Actions (in other words, can't do anything). Use a plugin like Yanfly's or Hime's to make these Destroyed enemies untargetable, as a convenience to the player. When all three enemies are KO'ed (you can check this using switches or conditional branches), remove the KO protection from all the enemies and the enemy will die. The cool thing about this approach is that you can visually represent each part being destroyed during the battle.
2) Use a battle background that has the (large, complete) enemy's sprite pasted onto it. Make the
actual enemies completely invisible and (if you're using a sideview battle system, or HP bar plugins, or anything else that's relevant to enemy positioning) position the invisible enemy sprites where they'd belong on the monster. This makes things really easy as the invisible enemy sprites won't try to "fade" (you can use Troop events to show animations if you want when each part is KO'ed to indicate it's been defeated) and will remove themselves from the target list automatically when KO'ed. When the whole boss is KO'ed, you will need to do something to remove the enemy's picture from the background - the best way I can think of to do this would be to use a "Show Picture" command (a Change Battle Background might also work but I'm not sure) to show a picture of the "empty" scenery (the background minus the monster) over the real battle background. Alternatively, you could just fade out the screen, play a loud sound effect, and have dialogue to indicate that the party destroyed the monster.