Have you checked out Joe's Scenery Clinic yet? He has some really good ideas.
I am partial to using foam, then carving it and using a wire brush to get the strata look, also some 200 grit sand paper will smooth it well. I also use the WS Foam putty to fill in areas. The Foan and carving are pretty mess free, the sanding and wire brush will make little foam stick to you pieces. The Foam putty is also pretty mess free. With foam you would layer it to the height you want and then carve away the pieces.
As you can see I am big on foam. Will their be a tunnel that the trains run through?