We developed a novel technique for fine material processing based on a localized atmospheric-pressure plasma jet (APPJ) using a scanning probe microscope equipped with a nanopipette. Using a nanopipette — a tapered glass capillary with an aperture of sub-micrometer diameter — as a nozzle makes it possible to localize the discharge area of the APPJ for fine surface processing. The nanopipette can also be used as a probe for a scanning probe microscope operated with shear-force feedback control, which is capable of positioning the pipette edge in the vicinity of material surfaces for APPJ processing and imaging of the processed surface. Sub-micrometer holes and line patterns were successfully processed on a photoresist film. It was possible to control the size of the processed patterns by varying the applied pulse voltage and the distance between the pipette and the surface.