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Surpervoxels are becoming increasingly popular in many point cloud processing applications. However, few methods have been devised specifically for generating compact supervoxels from unstructured three-dimensional (3D) point clouds. In this study, we aimed to generate high quality over-segmentation of point clouds. We propose a merge-swap optimization framework that solves any supervoxel generation problem formulated in energy minimization. In particular, we tailored an energy function that explicitly encourages regular and compact supervoxels with adaptive size control considering local geometric information of point clouds. We also provide two acceleration techniques to reduce the computational overhead. The performance of the proposed merge-swap optimization approach is superior to that of previous work in terms of thorough optimization, computational efficiency, and practical applicability to incorporating control of other properties of supervoxels. The experiments show that our approach produces supervoxels with better segmentation quality than two state-of-the-art methods on three public datasets.