In automotive, diagnostics is manditorily required to be performed on every ECU (Electronic Control Unit) to ensure that there is no any problem with the electronically controlled components of the vehicle. Today ECU is used in almost every vehicle as an electronic device. Recent automobiles consist of more than 80 ECU for different tasks such that every ECU or group of ECU will perform their dedicated functions. This paper explains about configuration of clock modules for microcontroller based on motor controller applications and also deals with the implementation of UDS (Unified Diagnostic Service) protocol according to the standard ISO 14229-1 which is being used by diagnostic system to communicate or to transfer the data between client & server.