You can also use ADE to exclude Autogen, use an exclusion rectangle rather than a polygon though, and have the sim running with your plane where the object is. In ADE (Airport Design Editor) Click the connect button top right, and you will see a crosshair depicting the planes position.
Put the plane at the corners or various reference poits of the building by slewing it in sim, at each point use the marker tool to put a cross mark so you can now see where the building is (sometime the buildings show in ADE sometimes they do not. for most buildings the presence of a small Exxclusion rectangle ios sufficient to remove them, so try that first, drag out a small rectangle (the yellow symbol)
and place it in the centre of the building, save it, compile it (you may need to save the flight, so you can reload back at the same place) end the flight, go to settings scenery library, click OK, the database rebuilds, compile the scenery in ADE, do the settings library thing again, load the flight, if the building has gone, job done, if not use several excludes to cover the thing.
The exclusion rectangle are always oriented north, they do not rotate, but they are very much better than the polygons at getting shot of autogen stuff.