This work presents a benchmarking study between Lagamine, an in-house developed finite element (FE) code, and COMSOL Multiphysics® (Comsol) commercial software in thermal analyses to investigate their capability in modeling complex manufacturing processes. For this purpose, two case studies, including a NAFEMS benchmark for heat transfer with convection and a Directed Energy Deposition (DED) of a bulk sample, were used as test cases. The simulation models using Lagamine and Comsol solvers for each case were described. The underlying algorithms and theories, as well as the soft-ware development, are investigated. The computational results indicate slight differ-ences between Lagamine and Comsol solutions in both case studies. For the NAFEMS test case, the results obtained with Comsol solver appear to be less dependent on the mesh size than those obtained with Lagamine. For the DED test case, within the chosen configurations of Lagamine and Comsol codes, the maximum difference in the highest peak temperatures obtained from the two codes is about 20%. From an engineering point of view, it is suggested to determine parameters of the FE model consistently with the selected FE code to provide the best match with experimental observations.