An automated method of cleaning the pipes of a plate washing system is provided. The plate washing system includes at least one manifold having a plurality of pipes configured to be provided within wells of a plate in order to wash the wells, an ultrasonic transducer mounted to a tank, and a control system. The plate washing system also includes sensors to sense the position of the pipes relative to plate and the tank, and the fluid level within the wells of the plate. The method includes dispensing fluid to the tank, submerging the tips of the pipes within the fluid, activating the ultrasonic transducer in order to vibrate the fluid, and aspirating the fluid from the tank. The control system may initiate a cleaning operation at the request of the user, at a scheduled interval, or when the level sensing system detects a decrease in instrument function.