This was a stop-motion short animation I think produced in the early 2000s. It took place in a series of concrete corridors in the walls of a deep cylindrical shaft into the earth. The inhabitants of this structure were looked down on by surface dwellers. The protagonist I think was leading some kind of expedition into the tunnels when, through some mishap, he ends up decapitated. One of the tunnel-dwellers saves him by reattaching his head to a new body(?), leaving him with amnesia, and he joins their community.
One characteristic and eerie scene I recall is the protagonist being chased through the tunnels by semi-humanoid monsters. To escape them, he leads them down a hallway he had encountered before, that has a series of boreholes in one wall. Out of the boreholes extend a network of red, fleshy veins that trail down the wall and across the floor. These act as tripwires for the large carnivorous worms that live in the boreholes; when touched the worms immediately erupt and tear apart the other monsters.
In the end the protagonist I think regains his memories and is disgusted with the tunnel-dwellers. By some mishap, he again is decapitated, and his head falls to the very bottom of the giant cylindrical shaft, where some large creature that lives there comes upon him and I think kills him.