A tunnel cannot be achieved with any kinds of planar surface tools.
That's primarily achieved by absolutely manually get into details with a 3d editor program. Or maybe you could paste pre-made tunnel models onto a deformed matrix in a way it looks fine. Hiding the intersections with creativity like clever texturing and vegetation...
-In.Dev.X: A unique heavy story based shoot'em ~6%
-CoreFleet: An underground commander unit based RTS ~15%
-TailsVSEggman: An Sonic themed RTS under development for idea presentation to Sega ~15%