Despite recent advances in computer aided design (CAD) based tools, spacecraft thermal analysis remains outside the realm of finite element method (FEM) based analysis. The primary complaints against FEM often cited are: 1.FEM is not based on physical principles. 2.FEM codes do not provide procedural modeling for heaters, heat pipes, or other abstract thermal control components. 3.Inadequate radiation analysis capabilities. 4.FEM codes generate inappropriately large thermal models. However, a failure on the part of existing FEM based codes does not invalidate the advantages of the Finite Element Method. Properly implemented, FEM based systems can have significant advantages.A simple first law interpretation of FEM is presented, and shows that finite difference (FD) and FEM meshes may co-exist in the same thermal model, and solved using traditional analyzers such as SINDA/FLUINT.A description of an integrated FD/FEM based system that efficiently satisfies all areas of spacecraft thermal analysis, including thermal radiation, is also presented.