Systems and methods for conducting thermal analysis in materials and devices having multiple thermal control zones are provided. Modem apparatuses, such as manifolds, generally have several thermal devices that introduce or remove heat at different rates from several different regions. Previous attempts to determine a thermal profile required constant guessing and an unknown number of simulations to arrive at an acceptable result. Further, since the number of simulations required is not known from the onset of the operation, the duration is unknown, which is often unsatisfactory to manufacturing personnel. Disclosed embodiments include the use of FEA to aid in designing and/or evaluating manifold systems. In one embodiment, finite element analysis is conducted to determine the heat flux caused upon other control zone by a thermal device in a specified control zone.