Automatic target recognition (ATR) is an ongoing topic of research for the Air Force. In this effort we develop, analyze and compare template matching and deep learning algorithms for use in the task of classifying occluded targets in light detection and ranging (LiDAR) data. Specifically, we analyze convolutional sparse representations (CSR) and convolutional neural networks (CNN). We explore the strengths and weaknesses of each algorithm separately, then improve the algorithms, and finally provide a comprehensive comparison of the developed tools. To conduct this final comparison, we improve the functionality of current LiDAR simulators to include our occlusion creator and parallelize our data simulation tools for use on the DoD High Performance Computers. Our results demonstrate that for this problem, a DenseNet trained with images containing representative clutter outperforms a basic CNN and the CSR approach.