Microwave radiation is widely used for heating tissues in hyperthermia or diathermy medical treatments. Usually, in such treatments, the tissue's temperature is used as feedback for the microwave generator power control and consequently, for the control of the whole heating process. The temperature can be measured by contact, or non-contact (IR or MW radiometry), techniques. Unfortunately, in both cases the temperature sensors are also heated by the microwave power field, altering the measured result and sometimes damaging the sensors and the electronics. Another disadvantage of the IR temperature measurement is the possibility of measuring only skin temperature, independently on the penetration depth of the thermal wave. In this paper we present an experimental method for tuning the microwave generator power and the irradiation sequence, necessary to generate the correct temperature inside the layered system, by measuring only the surface temperature. An experimental three layer phantom model, with immersed temperature sensors has been used. It was demonstrated that the microwave power at the generator output can be adjusted by analyzing the differences between the layers' temperatures (measured by a contact technique) and surface's temperatures of the phantom (measured by IR method).