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A draped polygon is interrupted by surface features.
Polygons are a string of X,Y, and sometimes Z coordinates that define the boundary of an area. No coordinates are stored for the internal area of the polygon. ArcScene uses the vertices of the polygon boundary to define its height in the scene. However no interpolation is done on the internal area of the polygon. If the surface has a spire or other feature higher than the height of the polygon's edge, the surface protrudes through the polygon.
Convert the polygons to rasters. Rasters draped over a surface are interpolated at the center of each cell; therefore, the entire area of the raster is interpolated.