I need to extrude a cicle feature to a given depth but the extrude transformer does not appear to work on an ellipse feature. Is there another way to tackle extruding this feature using FME?
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Try using the GeometryCoercer to coerce the feature to a polygon and see if that works for you.
On some difficult DWG geometry I have also used ArcStroker to convert to a better geometry for further processing.