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The integration of structure from motion (SFM) and unmanned aerial vehicle (UAV) technologies has allowed for the generation of very high-resolution three-dimensional (3D) point cloud data (up to millimeters) to detect and monitor surface changes. However, a bottleneck still exists in accurately and rapidly registering the point clouds at different times. The existing point cloud registration algorithms, such as the Iterative Closest Point (ICP) and the Fast Global Registration (FGR) method, were mainly developed for the registration of small and static point cloud data, and do not perform well when dealing with large point cloud data with potential changes over time. In particular, registering large data is computationally expensive, and the inclusion of changing objects reduces the accuracy of the registration. In this paper, we develop an AI-based workflow to ensure high-quality registration of the point clouds generated using UAV-collected photos. We first detect stable objects from the ortho-photo produced by the same set of UAV-collected photos to segment the point clouds of these objects. Registration is then performed only on the partial data with these stable objects. The application of this workflow using the UAV data collected from three erosion plots at the East Tennessee Research and Education Center indicates that our workflow outperforms the existing algorithms in both computational speed and accuracy. This AI-based workflow significantly improves computational efficiency and avoids the impact of changing objects for the registration of large point cloud data.