This article presents a potential image processing method for determining the in-plane geometrical distortion of a scanning tunneling microscope (STM) image and calibrating it using a regular crystalline lattice, and describes the results obtained in comparative length measurements in the range of about 1 μm using a regular crystalline lattice as a reference scale and a dual tunneling unit-STM (DTU-STM) as a detector. The method is based on two-dimensional fast Fourier transform analysis. The DTU-STM with oneX-Ystage and two tunneling units independently controlled in theZ-axis direction was utilized for comparative length measurement. To improve the measurement accuracy, the present method is used to process the raw images obtained from the DTU-STM. The results of experiments, in which the cleaved surface of highly oriented pyrolytic graphite is used as a reference scale for measurement of lengths on the order of 1 μm, demonstrate the feasibility of the present image processing method and the possibility of comparative length measurement with subnanometer resolution using the DTU-STM.