A multiscale data engine is configured to generate a three-dimensional (3D) environment based on a multiscale 3D dataset. The multiscale data engine is also configured to generate a spatial hierarchy within the 3D environment by selectively grouping 3D objects within the 3D environment. The multiscale data engine is further configured to identify specific 3D objects within the 3D environment in response to input received from an end-user and based on spatial properties associated with the 3D objects. The multiscale data engine is also configured to generate various navigation graphical user interfaces (GUIs) that allow the end-user to navigate the 3D environment.