A substrate transport empiric arm droop mapping apparatus for a substrate transport system of a processing tool, the mapping apparatus including a frame, an interface disposed on the frame forming datum features representative of a substrate transport space in the processing tool defined by the substrate transport system, a substrate transport arm, that is articulated and has a substrate holder, mounted to the frame in a predetermined relation to at least one of the datum features, and a registration system disposed with respect to the substrate transport arm and at least one datum feature so that the registration system registers, in an arm droop distance register, empiric arm droop distance, due to arm droop changes, between a first arm position and a second arm position different than the first arm position and in which the substrate holder is moved in the transport space along at least one axis of motion.