How can I make a hole in the terrain?

So here’s the deal. I have a model of an underground bunker that i made in Blender. It has a shaft with a ladder inside that serves as the entry point to the bunker. The shaft juts up above the rest of the model, so that it is above the ground when the rest of the bunker is underground. But what is happening is that the terrain goes through the model.

This means that there is a patch of terrain going straight through the middle of the entrance shaft. Is there a way to make a hole right there so that the terrain goes around the shaft, allowing the player to have access to the bunker, instead of going right through it?

from the comments

check my answer here for using the DepthMask shader on the Unity Wiki (example video)

You could have a trigger volume at the position of the plane. While the player is in the trigger zone, use IgnoreLayerCollision to allow the player to move through the terrain layer.

What you would do is have 2 custom layers; one for the Player, and one for the terrain.

Define the layers on the trigger script. If you use User layer 8 and 9, this would look like :

public var playerLayer : int = 8;
public var terrainLayer : int = 9;

The function to call on the trigger script is simply :

 // when player enters trigger
 Physics.IgnoreLayerCollision( playerLayer, terrainLayer, true ); // ignore collision between player and terrain
 // when player exits trigger
 Physics.IgnoreLayerCollision( playerLayer, terrainLayer, false ); // DOES NOT ignore collision between player and terrain