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I've downloaded OS MasterMap with the intention of extruding buildings to their respective heights. I wrongly assumed that I would receive shapefiles of the buildings which I'd then extrude using the height data in the attribute table but instead comes as a shapefile called 'TopographicArea'.

I've imported this shapefile and linked the included building heights csv file but how do I go about extracting just the buildings and extruding them to their heights?

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Have a look at the attribute data for the Topographic Area layer. Simply select all entities that have a theme of "(1:buildings)" (or the featurecode = 10021). You may want to save your selection to a separate shapefile for convenience.

In ArcScene follow the Help Documentation:

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