A veteran police officer has been charged with murder over the fatal shooting of a driver during a routine traffic stop in Windsor two years ago.

Leading Senior Constable Timothy Howard Baker, 44, appeared in the Melbourne Magistrates Court on Wednesday, charged with one count of murder over the death of Vlado Micetic, 46, on August 25, 2013.

Mr Baker is alleged to have shot Mr Micetic three times from close range during a traffic stop in Union Street, after Mr Micetic allegedly brandished a flick knife.

Mr Micetic, who had almost 100 criminal convictions before the age of 25, was pulled over in a white Hyundai with stolen plates.