Three-dimensional (3D) root system architecture (RSA) is a predominant factor in anchorage failure in trees. Only a few studies have used 3D laser scanners to evaluate RSA, but they do not check the accuracy of measurements. 3D laser scanners can quickly obtain RSA data, but the data are collected as a point cloud with a large number of points representing surfaces. The point cloud data must be converted into a set of interconnected axes and segments to compute the root system traits. The purposes of this study were: (i) to propose a new method for easily obtaining root point data as 3D coordinates and root diameters from point cloud data acquired by 3D laser scanner measurement; and (ii) to compare the accuracy of the data from main roots with intensive manual measurement. We scanned the excavated root systems of two Pinus thunbergii Parl. trees using a 3D laser scanner and neuTube software, which was developed for reconstructing the neuronal structure, to convert the point cloud data into root point data for reconstructing RSA. The reconstruction and traits of the RSA calculated from point cloud data were similar in accuracy to intensive manual measurements. Roots larger than 7 mm in diameter were accurately measured by the 3D laser scanner measurement. In the proposed method, the root point data were connected as a frustum of cones, so the reconstructed RSAs were simpler than the 3D root surfaces. However, the frustum of cones still showed the main coarse root segments correctly. We concluded that the proposed method could be applied to reconstruct the RSA and calculate traits using point cloud data of the root system, on the condition that it was possible to model both the stump and ovality of root sections.