No, ArcGIS 3D Analyst can use all the datasets supported by ArcGIS. If your data does not have explicit three-dimensional coordinates, you can drape it on other surface data, such as a digital elevation model (DEM), or you can extrude the features in a 3D thematic representation (e.g., sales districts extruded by sales with the height representing the amount of sales), or you can use feature attributes (eg: the measured height of your tree features) to drive 3D symbology. You can also use 3D Analyst geoprocessing tools to convert 2D data to 3D data, as needed.