In forestry research, for forest inventories or other applications which require accurate 3D information on the forest structure, a Terrestrial Laser Scanner (TLS) is an efficient tool for vegetation structure estimation. Light Detection and Ranging (LiDAR) can even provide high-resolution information in tree canopies due to its high penetration capability. Depending on the forest plot size, tree density, and structure, multiple TLS scans are acquired to cover the forest plot in all directions to avoid any voids in the dataset that are generated. However, while increasing the number of scans, we often tend to increase the data redundancy as we keep acquiring data for the same region from multiple scan positions. In this research, an extensive qualitative analysis was carried out to examine the capability and efficiency of TLS to generate canopy top points in six different scanning combinations. A total of nine scans were acquired for each forest plot, and from these nine scans, we made six different combinations to evaluate the 3D vegetation structure derived from each scan combination, such as Center Scans (CS), Four Corners Scans (FCS), Four Corners with Center Scans (FCwCS), Four Sides Center Scans (FSCS), Four Sides Center with Center Scans (FSCwCS), and All Nine Scans (ANS). We considered eight forest plots with dimensions of 25 m × 25 m, of which four plots were of medium tree density, and the other four had a high tree density. The forest plots are located in central Slovakia; European beech was the dominant tree species with a mixture of European oak, Silver fir, Norway spruce, and European hornbeam. Altogether, 487 trees were considered for this research. The quantification of tree canopy top points obtained from a TLS point cloud is very crucial as the point cloud is used to derive the Digital Surface Model (DSM) and Canopy Height Model (CHM). We also performed a statistical evaluation by calculating the differences in the canopy top points between ANS and the five other combinations and found that the most significantly different combination was FSCwCS respective to ANS. The Root Mean Squared Error (RMSE) of the deviations in tree canopy top points obtained for plots TLS_Plot1 and TLS_Plot2 ranged from 0.89 m to 14.98 m and 0.61 m to 7.78 m, respectively. The relative Root Mean Squared Error (rRMSE) obtained for plots TLS_Plot1 and TLS_Plot2 ranged from 0.15% to 2.48% and 0.096% to 1.22%, respectively.