A three dimensional printer is configured to move at least one printhead from an area where the printhead is forming an object to a position opposite a shaft. The at least one printhead is operated to eject material onto the shaft and the shaft is rotated to enable a light sensor to generate signals indicative of a height of material at a plurality of positions on the shaft. The signals are compared to an expected height of material at each position to identify inoperative inkjets in the at least one printhead.