Microprocessor and Microcontroller based circuits normally use high frequency crystals In general, there will be a number of data lines on such a Printed Circuit Board if is observed that, if special care is not taken in the layout of the Printed Circuit Board (PCB), it is most likely to generate electromagnetic interference. It is very common to have EMI-hot zones on such a PCB; some of the ground islands may become very noisy and this has been observed in our case study of the microprocessor based Printed Circuit Board In such a case, because of generation of Common Mode Current, the circuit will give intermittent errors like those we have experienced in our case study and it may fail in the long run as the ICs are vulnerable to EMI. This paper deals in derail about the generation of common mode current as a source of EMI and its effects The analysis of the generation of the Common Mode Current is also covered in the paper. The protection measures to contain EMI in the High Frequency Printed Circuit Board are also analysed for reduction of EMI effect during the design of the PCB. in our case the system consists of two sub-systems, viz, the display unit and the control unit. Particularly the EMI emission pattern from the hot zones is presented graphically. EMT emissions both conducted and radiated before and after application of control measures have been taken in accordance with the FCC Class B Operation.