Nowadays, additive manufacturing via topology optimization creates new opportunities for weight reductions in aerospace industry where high fly-to-buy ratio is desired. Selective laser sintering of advanced engineering materials like nickel super alloys are also expanding to reduce the cost and time of the manufacturing in aerospace industry. Elevated temperature and temperature gradients are critical factors in selective laser sintering of metals and they significantly affect the quality and integrity factors of produced parts such as microstructures, porosity, residual stresses, and distortions. Therefore, the aerospace industry needs advanced simulation tools to predict the temperatures, temperature gradients, and molten pool geometries to better understand the physics of the selective laser melting process as well as for the process optimizations. This article introduces an adjustable finite element-based multi-physics and multi-software platform thermal model, for laser additive manufacturing in powder bed systems to predict the transient temperature and the molten pool geometry. The developed model is able to simulate 3D transient temperature and molten pool shape in the laser additive manufacturing process by including the features of melting and solidification, porous media, and temperature-dependent thermal material properties for different materials. A set of experiments of Inconel 625 is carried out in order to measure the size of the molten pool and to validate the developed thermal model. An experimental study on temperature distribution carried out with titanium and an experimental study on molten pool sizes carried out with Inconel 625 in the literature are also compared with the developed thermal model. The estimation errors of the developed model are in the range of 11–18%.