A method and apparatus for generating and displaying a 3D representation of a portion an intraoral scene is provided. The method includes determining 3D point cloud data representing a part of an intraoral scene in a point cloud coordinate space. A colour image of the same part of the intraoral scene is acquired in camera coordinate space. The colour image elements are labelled that are within a region of the image representing a surface of said intraoral scene, which should preferably not be included in said 3D representation. A labelled and applicably transformed colour image is then mapped onto the 3D point cloud data, whereby the 3D point cloud data points that map onto labelled colour image elements are removed or filtered out. A 3D representation is generated from said filtered 3D point cloud data, which does not include any of the surfaces represented by the labelled colour image elements.
