The invention relates to a method and apparatus forgenerating and displaying a 3D representation of at least a portion anintraoral scene. The method includes determining 3D point cloud datarepresenting a part of an intraoral scene in a point cloud coordinatespace. A colour image of the same part of the intraoral scene isacquired in camera coordinate space. The colour image elements arelabelled that are within a region of the image representing a surface ofsaid intraoral scene, which should preferably not be included in said3D representation. Typically, image elements are labelled within aregion with either a colour or colour pattern corresponding to a surfacecolour or surface colour pattern of a utensil used intraorally whenacquiring said 3D data and colour image. Alternatively, or in additionelements are labelled that are within a region having a colour patterncorresponding to a colour pattern of a tooth surface area comprisingundesired stains or particles. Either before or after said labelling of theimage elements, the colour image is, if necessary, transformed fromthe camera coordinate space to the point cloud coordinate space. Thelabelled and applicably transformed colour image is then mapped ontothe 3D point cloud data, whereby the 3D point cloud data points thatmap onto such labelled colour image elements are removed or filteredout. Eventually, a 3D representation is generated from said filtered 3Dpoint cloud data, which does not include any of the surfaces representedby the labelled colour image elements.
