We report on the measurement of the fringe-to-substrate phase error in our Nanoruler system. This system utilizes scanning beam interference lithography to pattern and measure large-area, nanometer-accuracy gratings that are appropriate for semiconductor and integrated opto-electronic metrology. We present the Nanonruler's metrology system that is based on digital frequency synthesizers, acousto-optics, and heterodyne phase sensing. It is used to assess the fringe-to-substrate placement stability and the accuracy of the feedback signals. The metrology system can perform measurements in real time, on the fly, and at arbitrary locations on the substrate. Experimental measurements are presented that demonstrate the nanometer-level repeatability of the system. Dominant error sources are highlighted. © 2003 American Vacuum Society.