Counterfeiting of integrated circuits (IC) has become a serious concern for electronics manufacturers, system integrators, and end users. It is necessary to find a robust solution which is both efficient and low cost in terms of implementation in order to detect and avoid the counterfeiting of ICs. To combat the counterfeiting of ICs in this paper we have extended our previous work on utilizing radiated EM emission for authentication of IC on microcontroller boards. Our proposed scheme exploits manufacturing based process variation (PV), which continues to dominate in the nanoscale technologies. We have focused our work on authentication of microcontrollers which are one of the main targets of counterfeiting. The proposed work emphasizes on being non-intrusive and does not require any internal modification of the system on chip, it can be used on already deployed ICs. Generated EM response is treated to different encoding metrics to quantize it as a fingerprint for the IC. To validate our proposed scheme, measurements are carried out over several microcontroller boards.