I am looking to subtract Surface from Surface as shown in the diagram.

The water surface is one large Surface. The surface representing the terrain is a PolySurface, which is a combination of various Surfaces.

How can we subtract the PolySurface representing the topography from the surface representing the water surface to obtain the water surface as shown in the figure?

I am assuming this will be done in Dynamo.

I would appreciate it if you could lend me your thoughts.

Geometry.Split node should do the trick. May be slow if your topography surface is complex or large - simplify if you can.

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Thanks for the reply.

I was able to cut out the water surface by using Geometry.Split.

However, if I take an area of the water surface that is larger than the PolySurface of the terrain, I could not cut out the Surface.

Is there any requirement that the Surface of the water surface be smaller than the PolySurface of the terrain?

Not sure what you mean; can you construct a simple design script based example?