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This paper concerns the optimization and performance analysis of an automatic control algorithm for managing power output of large multielement array hyperthermia applicators. Simulation and corresponding measurement of controller performance in a solid tissue equivalent phantom model is utilized for analysis of controller response to dynamically varying thermal load conditions that simulate clinical treatments. The analysis leads to an optimum controller which demonstrates the ability to achieve a uniform and stable temperature profile over a large surface area regardless of surrounding thermal load. This paper presents several advancements to the performance of a previously published control routine, including: 1) simplified simulation techniques for thorough characterization of controller performance; 2) an optimization procedure leading to an improved hybrid control algorithm for maintaining optimal performance during periods of both "rising" and "steady-state" temperature; 3) performance analysis of a control algorithm tailored for large area hyperthermia treatments with a mulitelement array applicator. The optimized hybrid controller is applied to the conformal microwave array (CMA) hyperthermia system previously developed for heating large area surface disease such as diffuse chestwall recurrence of breast carcinoma, and shown to produce stable, uniform temperatures under the multielement array applicator for all thermal load conditions.