We present a mechanism for directly positioning the tip over a micron-size sample by tracking the trajectory of the tip and tip shadow. A bilayer graphene sheet identified by Raman spectroscopy with a lateral size of 20 μm × 50 μm was transferred on the surface of shaped gold electrodes, on which it will be rapidly captured by a homebuilt scanning tunneling microscopy (STM) with the help of an optical microscope. Using the improved line-based imaging mode, atomic-resolution images featuring a hexagonal lattice structure on the bilayer graphene sheet were obtained by our positioning-capable STM. We have also observed a unique O-ring superstructure on graphene surface that caused by the collective interference near the boundaries or defects. Furthermore, we successfully captured a graphene sheet of size as small as 1.3 nm by a rapid and large-area searching operation; this is the first time that such a small graphene sheet has been observed with atomic resolution. The STM images of a micron-size graphene sheet illustrate the significant positioning ability and imaging precision of our homebuilt STM. Our results contribute to further STM studies on samples with ultra-small size.