A system and method for cleaning probe pins on a probe card used in testing a semiconductor device during fabrication thereof. A ceramic cleaning wafer is utilized to clean the probe pins without having to remove the probe card from a production line. The same apparatus used to test production wafers also handles the cleaning wafer during a probe cleaning cycle. During operation of the cleaning cycle, the cleaning wafer is placed in a manual load tray, which inserts the cleaning wafer into a prober machine. The cleaning wafer is transported by a robotic trolley to a prealign stage area where the cleaning wafer is aligned and centered. The cleaning wafer is then placed on a support device. The support device and cleaning wafer are positioned under a pneumatic sensor and profiled to determine wafer planarity. The support device and cleaning wafer are then positioned underneath the probe pins on the probe card to be cleaned. Thereafter, the z-axis distance between the probe pins and the surface of the cleaning wafer is decreased such that the probe pins contact the cleaning wafer, thereby removing debris from the probe pins. The cleaning wafer is then removed from the support device when cleaning of the probe pins has been completed.