The crystalline lattice and periodic grating features have been employed as reference scales for simultaneous calibration between the scanning tunneling microscope (STM) and atomic force microscope (AFM). This article describes the configuration and functions of a dual unit STM-AFM for length metrology. The system was developed on the basis of a dual tunneling unit STM (DTU-STM) in view of the fact that the application of DTU-STM was strongly limited by sample conductivity. In the dual unit STM-AFM, a STM serving as a reference unit and an AFM as a test unit were combined by using one singleXYscanner. Both the reference sample and the test sample were installed at the center of the scanner on either surface, and were imaged by STM and AFM units at the same time. The length of the test sample image was measured by counting the periodic features of the reference sample image. We present a detailed discussion about the structure and control of the dual unit STM-AFM. Some comparison results, respectively, using crystalline lattices and periodic grating features as reference scales for length calibration of test samples are also provided. Experiments show a satisfactory matching between the STM unit and the AFM unit when covering a wide scan range from 5 nm to 10μm. Using different standard reference scales, the system enables nanometer and/or sub-micron accuracy length metrology of microstructures with any conductivity.