In this article, a multi-view registration approach for the 3D handheld profiling system based on the multiple shot structured light technique is proposed. The multi-view registration approach is categorized into coarse registration and point cloud refinement using the iterative closest point (ICP) algorithm. Coarse registration of multiple point clouds was performed using relative orientation and translation parameters estimated via homography-based visual navigation. The proposed system was evaluated using an artificial human skull and a paper box object. For the quantitative evaluation of the accuracy of a single 3D scan, a paper box was reconstructed, and the mean errors in its height and breadth were found to be 9.4 μm and 23 μm, respectively. A comprehensive quantitative evaluation and comparison of proposed algorithm was performed with other variants of ICP. The root mean square error for the ICP algorithm to register a pair of point clouds of the skull object was also found to be less than 1 mm.