A polymerase chain reaction (PCR) micro-chip with integrated thin film heaters and temperature detectors has been realized on a silicon-SOG-PDMS (polydi( methyl) siloxane) platform. Accurate temperature sensing and control is important for a PCR reaction. This precludes the placement of the temperature sensor anywhere else but within the PCR chamber which can, in certain microchip designs complicate the fabrication methodology. This paper presents the design and optimal placement of a thin film resistance based temperature detector (RTD) for sensing of temperature response on the bottom of the chip (heater side) and predicting the temperature response on the top of the chip (PCR chamber side). Thermal modeling of the system has been performed using a parametric blackbox approach based on the input-output data. From the steady state response of the system, Pseudo random binary sequences (PRBS) have been generated and used to excite it. Second and fourth order ARX (Auto regressive with exogenous inputs) models have been derived for optimal control and their performances have been compared. Reduction of fabrication complexity in regards to optimal placement of temperature sensor has been proposed.