For most large 3D engineering models, the instance positions of repeating instances of connected components show significant multiple spatial aggregation. The invention uses several KD-trees, each for one cluster of points which are spatially aggregated. The multiple KD-trees generate a relatively short data stream, and thus improve the total compression ratio. A method for encoding points of a 3D mesh model comprises steps of determining that the mesh model comprises repeating instances of a connected component, and determining for each repeating instance at least one reference point, clustering the reference points of the repeating instances into one or more clusters, and encoding the clustered reference points using KD-tree coding, wherein for each cluster a separate KD-tree is generated.