Currently, 3D point clouds are obtained via LiDAR (Light Detection and Ranging) sensors to compute vegetation parameters to enhance agricultural operations. However, such a point cloud is intrinsically dependent on the GNSS (global navigation satellite system) antenna used to have absolute positioning of the sensor within the grove. Therefore, the error associated with the GNSS receiver is propagated to the LiDAR readings and, thus, to the crown or orchard parameters. In this work, we first describe the error propagation of GNSS over the laser scan measurements. Second, we present our proposal to overcome this effect based only on the LiDAR readings. Such a proposal uses a scan matching approach to reduce the error associated with the GNSS receiver. To accomplish such purpose, we fuse the information from the scan matching estimations with the GNSS measurements. In the experiments, we statistically analyze the dependence of the grove parameters extracted from the 3D point cloud -specifically crown surface area, crown volume, and crown porosity- to the localization error. We carried out 150 trials with positioning errors ranging from 0.01 meters (ground truth) to 2 meters. When using only GNSS as a localization system, the results showed that errors associated with the estimation of vegetation parameters increased more than 100 % when positioning error was equal or bigger than 1 meter. On the other hand, when our proposal was used as a localization system, the results showed that for the same case of 1 meter, the estimation of orchard parameters improved in 20 % overall. However, in lower positioning errors of the GNSS, the estimation of orchard parameters were improved up to 50% overall. These results suggest that our work could lead to better decisions in agricultural operations, which are based on foliar parameter measurements, without the use of external hardware.