I'm not sure I understand your question;

I shall try to clarify what the pictures are.
The model pictured at:
http://www.trainsarefun.com/temp/AT_Vanderbilt%20ShapeView.jpgis the model as displayed by ShapeFileViewer (SFV)
The other pictures kindly hosted by Steve are MSTS screen grabs of the Vanderbuilt Yard near the Flatbush Avenue Terminal. (No I will never call it 'Atlantic Terminal')
So yes, the models are compatable with MSTS as is the other picture
of the Bay Ridge division East New York south tunnel portal.
Each model is a single shape I built with the freeware modeling program, Google SketchUp.
The GSU model was exported to an MSTS shape file using the exporter written by Paul Gausden (Decapod)
It is available here:
http://www31.brinkster.com/decapod/ Google Sketch is an absolutly easy to use VERY user friendly 3D modeling program that is just perfect for making trackside structures.
You can use photos of the structures to 'paint' the model.
Is so just perfect and I wouldn't be a-building the LIRR without it. Just look at the McCauley Potato building(s).
A unique set of three buildings that took a few hours to cobble together into a 248 poly model.
If you want to make accurate models for your TrainSim route and were afraid to get into 3D modeling, well, you don't know what you are missing. The true joy of being able to build those little models that make a route complete.
Get SketchUp and also download all the Materials Libraries that go with it.
Then, and this is important; You MUST run through the Tutorials.
Do this and you are on the way to making models with the first (not kidding here) Truly Intelligent 3D modeling program that actually tries to 'help' you as you draw!
Enjoy!