The Entropy Generation Minimization (EGM) approach is applied to the design of a new integrated radar aircraft skin, which both meets requisite aircraft structural needs and provides a pathway for the waste heat from structurally integrated power devices. Thermoelectric (TE) devices, sandwiched between a heterogeneous skin layer and the radar devices for the purpose of harvesting waste heat rejected to the ambient, are considered in the analysis. A heterogeneous skin layer is designed using the EGM approach, which is then applied to the overall mission of the aircraft to determine the optimal skin thickness and volume fractions of the matrix and inclusions in the composite skin.