The effective development of digital twins of real-world objects requires sophisticated data collection techniques and algorithms for the automated modeling of individual objects. In City Information Modeling (CIM) systems, individual buildings can be modeled automatically at the second Level of Detail or LOD2. Similarly, for Tree Information Modeling (TIM) and building Forest Digital Twins (FDT), automated solutions for the 3D modeling of individual trees at different levels of detail are required. The existing algorithms support the automated modeling of trees by generating models of the canopy and the lower part of the trunk. Our argument for this work is that the structure of tree trunk and branches is as important as canopy shape. As such, the aim of the research is to develop an algorithm for automatically modeling tree trunks based on data from point clouds obtained through laser scanning. Aiming to generate 3D models of tree trunks, the suggested approach starts with extracting the trunk point cloud, which is then segmented into single stems. Subsets of point clouds, representing individual branches, are measured using Airborne Laser Scanning (ALS) and Terrestrial Laser Scanning (TLS). Trunks and branches are generated by fitting cylinders to the layered subsets of the point cloud. The individual stems are modeled by a structure of slices. The accuracy of the model is calculated by determining the fitness of cylinders to the point cloud. Despite the huge variation in trunk geometric forms, the proposed modeling approach can gain an accuracy of better than 4 cm in the constructed tree trunk models. As the developed tree models are represented in a matrix format, the solution enables automatic comparisons of tree elements over time, which is necessary for monitoring changes in forest stands. Due to the existence of large variations in tree trunk geometry, the performance of the proposed modeling approach deserves further investigation on its generality to other types of trees in multiple areas.