In this paper, we present technique to fabricate nanopatterns on Cu thin films via an electrochemical nanomachining (ECN) using an atomic force microscope (AFM). A conductive AFM cantilever tip (Pt/Ir5 coated) was used to form an electric field between tip and Cu substrate with applying a voltage pulse, resulting in the generation of an etched nanopattern. In order to precisely construct the nanopatterns, an ultra-short pulse was applied onto the Cu film through the AFM cantilever tip. The line width of the nanopatterns (the lateral dimension) increased with increased pulse amplitude, on-time, and frequency. The tip velocity effect on the nanopattern line width was also investigated that the line width is decreased with increasing tip velocity. Experimental results were compared with an equivalent electrochemical circuit model representing an ECN technique. The study described here provides important insight for fabricating nanopatterns precisely using electrochemical methods with an AFM cantilever tip.