Where can you find a Molten Core?
Solution 1:
I fought the Penguin UFO last night. You can get it from him. A nice tactic is to use your universal tool and trap him with dirt, so he doesn't spawn penguins. Just hold him in place while you kill him.
To spawn a Penguin UFO, Use a distress signal
Solution 2:
As link says, it's rare drop of Penguin UFO. However, I haven't get that yet.