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A global registration is often insufficient for estimating dendrometric characteristics of trees because individual branches of the same tree may exhibit different positions between two scanning procedures. Therefore, we introduce a localized approach to register point clouds of botanic trees. Given two roughly registered point clouds PC1 and PC2 of a tree, we apply a skeletonization method to both point clouds. Based on these two skeletons, initial correspondences between branch segments of both point clouds are established to estimate local transformation parameters. The transformation estimation relies on minimizing the distance between the points in PC1 and the skeleton of PC2. The performance of the method is demonstrated on two example trees. It is shown that significant improvements can be achieved for the registration of fine branches. These improvements are quantified as the residual point-to-line distances before and after the localized fine registration. In our experiment, the residual error after the local registration is on an average of 5 mm over 90 skeleton segments, which is about three times smaller than the average residual error of the initial rough registration.