A small-size scanning tunnel microscope (STM) developed to provide an easy operation for both tip and sample setting is applied to three-dimensional topographic measurements of microlithography patterns. The patterns having a grid structure with 160 nm in periodicity, 20–30 nm in groove width, and 40–50 nm in groove depth are fabricated on Si substrates using a technique of enhanced chemical etching by focused ion beam. The STM images are compared with two-dimensional scanning electron microscope images. Fairly good resolution of topographic maps for a large area is obtained for the fine groove structures. The large-area images are further processed to correct the piezoscanners’ nonlinearity, which becomes conspicuous for large-area scanning.