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Besides their important place in space education, the significance of CubeSats as technological and scientific demonstrators is also increasing, due to the miniaturization and their low cost associated with the maturing CubeSat technology. The primary energy sources for these spacecraft are solar cells. It is a key question to maximize the available electrical energy gained from the minimal solar cell area available, while coping with the extreme thermal conditions of space which the panels are exposed to. In this paper we describe the structural design of solar cell arrays aimed at maximal energy yield in space along with the thermal characterization techniques used during the thermal optimization of the structure. The presented procedure resulted in an enhanced solar array design which was successfully used in the Masat-1 CubeSat mission, supported by flight telemetry data regarding solar cell temperature values.