In Bentley Pointools If your converted POD file includes classification then you can use the Layer from classification option. This will create a new layer based on the classification in the point cloud and all points in the classification will be placed on that layer. To create a a classified POD file. you will need to create a number of layers as required for your classification and then move the points to each layer. Once you have done this you can save your project and export to a new POD file using the Export option "layers as classes"
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