Hmm... maybe "The Last Starfighter?" There's an alien bounty hunter in it that goes after the film's hero on Earth. It is pretty fugly, and ends up doing battle with the robotic clone of the "Last Starfighter" before getting blowed up real good.
Is this the thing that has haunted you since childhood?
Wow, great thinking on that one, Jordan. The alien assassins (zandozan) are pretty freaky, and is a good possibility.