I was doing some research in relation to this question, and I realized that I had run into a snag. I'm not aware of any rules in either D&D 3.5 or Pathfinder that directly relate to creating buildings underground.
I'm aware of the downtime rules, but the process to create buildings using these rules has a number of assumptions that make them non-helpful to me, namely that they assume that you're building in an existing town, and that there is no mention of how the rules would work underground.
I'm also aware of the Stronghold Builder's Guide, but I no longer have a copy, so I can't find out if there are specific rules about underground structures there.
Are there any rules for building structures in 3.5 or PF that specifically address building those structures underground?
Best Answer
You are correct in assuming the stronghold builder's guide contains the information you are looking for. It has information on the costs of building below ground, including successive costs for deeper layers, and the difference between turning a cave of appropriate size and shape vs new excavations.
It costs an extra 10% to create an underground structure, though any hewn stone walls needed are free. There is an additional surcharge for each room built below the first subterranean layer, which is detailed on page 33 of the Stronghold Builder's Guide.
The Stronghold Builder's guide is 3.0, but with the exception of a few spell effects for wondrous architecture, is still the best official source.