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FME's SurfaceModeller transformer does not use boundary features, nor can the Clipper clip the output 3D surfaces. However, the workaround described below allows you to effectively clip the SurfaceModeller output to an irregular boundary.
The triangles output by the SurfaceModeller are standard polygons rather than 3D surface, and can be clipped by the Clipper. However, the clipping boundary must be draped to the ground first, since any vertices added to the triangles will derive their elevation from the clipping boundary. Luckily, we can drape the clipping boundary at the same time as we create the surface triangles.
After clipping the triangles, we use a FaceReplacer to turn them into 3D surfaces, then an Aggregator to create a multi-surface suitable for writing out to most of FME's 3D writers. However, a mesh is much more efficient representation than a multi-surface, so we can use a Triangulator to convert the multi-surface into a mesh.
The attached workspace template illustrates the process. Templates contain source data as well as the workspace, and can be opened in Workbench exactly the same as workspace files.
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