Polygon Layer Overlaps DEM at Full Extent Despite its Elevation being lower in Scene view using ArcGIS Pro.

Solución alternativa

Clip the polygon and only keep the area where the elevation of polygon is more than the dem. 

Below are the steps:

• Extract by Attribute Tool

1. Use the DEM raster layer as the input.
2. Set the clause to: Value = 0 OR Value = 1.
3. Specify an appropriate name for the output raster, then execute the tool.

• Raster to Polygon Tool

1. Convert the raster output from Step 1 into a polygon feature class.
2. Use the Value field during conversion.
3. Run the tool with default settings.

• Intersect Tool

1. Use the polygon layer created in Step 2 and another relevant polygon layer as input features.
2. Maintain default parameters.
3. Execute the tool to generate the intersected output.
4. Now enable the Dem layer and the clipped Polygon created from the intersect tool.

Pasos para reproducir