Growing evaluation in the early stages of crop development can be critical to eventual yield. Point clouds have been used for this purpose in tasks such as detection, characterization, phenotyping, and prediction on different crops with terrestrial mapping platforms based on laser scanning. 3D model generation requires the use of specialized measurement equipment, which limits access to this technology because of their complex and high cost, both hardware elements and data processing software. An unmanned 3D reconstruction mapping system of orchards or small crops has been developed to support the determination of morphological indices, allowing the individual calculation of the height and radius of the canopy of the trees to monitor plant growth. This paper presents the details on each development stage of a low-cost mapping system which integrates an Unmanned Ground Vehicle UGV and a 2D LiDAR to generate 3D point clouds. The sensing system for the data collection was developed from the design in mechanical, electronic, control, and software layers. The validation test was carried out on a citrus crop section by a comparison of distance and canopy height values obtained from our generated point cloud concerning the reference values obtained with a photogrammetry method. A 3D crop map was generated to provide a graphical view of the density of tree canopies in different sections which led to the determination of individual plant characteristics using a Python-assisted tool. Field evaluation results showed plant individual tree height and crown diameter with a root mean square error of around 30.8 and 45.7 cm between point cloud data and reference values.