I think I just figured this out today, but I haven't actually tried it. I think you need to create lines at the surface (not sure it matters if they are 3d or not), then set the base height somewhere above your surface elevation (just to make sure it cuts everything), then extrude that line down into the subsurface as far as you need to cut through all your layers. Then, I think you could use the Intersect 3D tool.
Does that help?