The role of forests is increasing because of rapid land use changes worldwide that have implications on ecosystems and the carbon cycle. Therefore, it is necessary to obtain accurate information about forests and build forest inventories. However, it is difficult to assess the internal structure of the forest through 2D remote sensing techniques and fieldwork. In this aspect, we proposed a method for estimating the vertical structure of forests based on full-waveform light detection and ranging (FW LiDAR) data in this study. Voxel-based tree point density maps were generated by estimating the number of canopy height points in each voxel grid from the raster digital terrain model (DTM) and canopy height points after pre-processing the LiDAR point clouds. We applied an unsupervised classification algorithm to the voxel-based tree point density maps and identified seven classes by profile pattern analysis for the forest vertical types. The classification accuracy was found to be 72.73% from the validation from 11 field investigation sites, which was additionally confirmed through comparative analysis with aerial images. Based on this pre-classification reference map, which is assumed to be ground truths, the deep neural network (DNN) model was finally applied to perform the final classification. As a result of accuracy assessment, it showed accuracy of 92.72% with a good performance. These results demonstrate the potential of vertical structure estimation for extensive forests using FW LiDAR data and that the distinction between one-storied and two-storied forests can be clearly represented. This technique is expected to contribute to efficient and effective management of forests based on accurate information derived from the proposed method.