An alignment tool, method and system are provided for aligning a cassette handler to a robot blade in a workpiece handling system, in which the tool comprises a frame or fixture adapted to be supported by the cassette handler support surface, in which the frame has one or more distance sensors positioned to measure the distance of a workpiece or robot blade from the sensor or a predetermined reference point or surface. In a preferred embodiment, the frame emulates a workpiece cassette and the distance sensors provide a numerical output of the distance to the workpiece. As explained in greater detail below, these distance measurements facilitate accurately leveling and aligning the cassette handler support surface relative to a workpiece supported by the robot blade such that when the frame is replaced by an actual workpiece cassette, the workpiece cassette will also be level and aligned with respect to the robot blade and the workpiece held by the blade. As a consequence, accidental scratching and breakage of workpieces such as semiconductor wafers and display substrates may be reduced or eliminated.