Got my HO G43 from Tangent, getting ready to start my CAD drawing for a Shapeways N scale version. I've never done any projects like this so will have questions. One of those is will the corrugations be a problem do to their small size? Also do I just need to create a 3D cad file? Those are just a few early questions.
I don't see an issue with the corrugations apart from possible rendering issues depending on what material you use. Anything that sticks out from a flat surface could create a lot of artifacts from the support material with FUD/FXD.
One of the first things to think about is if you want to make a flat kit or render it all as one. If you're planning on using FUD/FXD I say to design it as a kit and hope you can get it rendered flat. If you want to try the new HDA in one piece, the minimum wall thickness could come into issue. I should have my first caboose printed in HDA in a week or two and I had to fatten up a few areas to get it to pass all the checks.
As for the file, Shapeways is pretty open, but I would recommend that what ever you do is a solid model. The most common file type for this is .stl.
Jason