Can I cut through terrain?

Specifically can I just cut a hole through it?

I had planned to have an elaborate set of tunnels underground with a hatch that led above ground but when I went to punch my hole in the terrain for the hatch I realized that using the sculpting tools like Surface etc., all I can do is hollow out the terrain ... meaning that I have to carefully follow every pipe underground all the way to the end to keep from walling off my tunnels.

Is there a simple way to just cut a hole in the terrain?

For instance if I wanted to run a pipe through a mountain could I just put the pipe through the mountain and somehow stamp a hole through just the two sides of the mountain rather than burrowing all the way through?

I was wondering about this too.

I don't think so, but what you could do is drag the cylinder shape onto the terrain sculpt brush, set it to destructive mode, and then use the advanced properties to scale and rotate it to the size hole you need and use it to punch through the mountain in one go. Then just run your pipe through the tunnel you've made.