In this article tracking and stepping control of the tip position of a scanning tunneling microscope (STM) by referring to atomic points and arrays on a regular crystalline surface which is used as a two-dimensional reference scale is described. Highly oriented pyrolytic graphite (HOPG) crystal, whose lattice spacing is approximately 0.25 nm, was used as the reference. To utilize the topographic features on the crystalline surface as a reference, a method for determining two-dimensional lateral gradient signals, i.e., the X, and Y axes gradient signals, of the crystalline surface was applied to the control. A rigid STM consisting of a tip scanner and a sample XY stage, and control instruments were developed. The X and Y axes gradient signals were obtained simultaneously using two-phase lock-in modulations of a tunneling current modulated with circular dither motion applied to the tip XY scanner. Modulation frequency and amplitude of the tip were 1 kHz and less than 0.04 nm, respectively. The sample XY stage was controlled for tip positioning by feedback of the X and Y axis gradient signals. First, the tracking control of the STM tip onto an atomic point of the HOPG surface for a maximum duration of about 10 min was performed. Second, tracking and motion control of the STM tip along a crystalline axis of the HOPG surface was demonstrated. The STM tip continued “back and forth” motion along the crystalline axis of the HOPG surface for a maximum duration of 200 s with a maximum tip speed of 6 nm/s. The maximum displacement deviation from the crystalline axis was less than 1/3 lattice spacing (∼0.08 nm). Third, the quantized stepping of the STM tip with lattice spacing stepping with a repetitive rate of 0.5 Hz along the crystalline axis was examined. The maximum displacement deviation from the crystalline axis was less than 1/2 lattice spacing (∼0.12 nm). The feasibility of tracking and stepping control of the STM tip position by referring to atomic points and arrays was confirmed, and the proposed method can be applied to real-time length measurement with subnanometer resolution using a regular crystalline lattice. © 1999 American Institute of Physics.