A self-teaching robot arm positioning method that compensates for support structure component alignment offset entails the use of a component emulating fixture preferably having mounting features that are matable to support structure mounting elements. Robot arm mechanism motor angular position data measured relative to component emulating fixture features are substituted into stored mathematical expressions representing robot arm vector motion to provide robot arm position output information. This information indicates whether the actual relative alignment between the robot arm mechanism and a semiconductor wafer carrier is offset from a nominal relative alignment. The robot arm mechanism position output information can be used to effect either manual or automatic correction of an offset from the nominal relative alignment.