Metrology tools with the ability to measure spindle motion error on the order of a nanometer are required due to recent advances in nanotechnology. We propose a direct measurement method for the radial motion error of a precision spindle using a regular crystalline lattice and a scanning tunneling microscope (STM). A highly oriented pyrolytic graphite (HOPG) crystal combined with an STM is used as a two-dimensional reference scale. The measurement principle and the preliminary experimental results are discussed in this article. The preliminary experimental results demonstrated that the proposed method has the capability to incorporate a two-dimensional encoder to measure the spindle motion error.