I've tried changing the colour of the surface, then saving the modified window as a template. When it's reloaded, the fill has reverted to red. I've tried changing the settings on the fundamental 3d.otp and mesh.otp templates, by loading them, putting data in, changing the colour and saving. Again, when they're reloaded and new data is put back in, they're red again.

I'm successfully using a similar command to the one you suggest in my script, to put data into pre-generated templates. The surface plots fine, but in the wrong colour, and that seems to be un-definable.

1. Plot any matrix as any of the 3D plot types: Fill Surface, Wire Surface, Wire Frame or Colormap Surface.
   
2. Make any changes you like
   
3. Select File:Save Template As... from the menu (Save as MY3D.OTP for example)
   

// First create a Graph window based on one of your pre-defined templates
window -t plot MyTemplate1 MyWinName;
// Now add some data
layer.include(matrix1, 242);
// The above method doesn't auto-rescale so..,
layer -a;
// Add another layer, based on another (or the same) template
page -l MyTemplate2;
// The new layer is now the active layer
// Now add the data
layer.include(matrix2, 242);
// And again, rescale
layer -a;
// Repeat the previous three commands as needed
// Now arrange the layers
run.section(graph,ArrangeAllLayers);