The coupling AFM lithography is innovatively developed to fabricate the controllable 2.5D area structures on the conductive sample surface with the nanoscale resolution, which has wide applications in the fabrication of various nanodevices. The AFM probe functions as both the cutting tool and the electrode tool during the coupling AFM lithography processes. Compared to the conventional mechanical AFM lithography or electric AFM lithography, which merely applies force load or bias voltage, the coupling AFM lithography owns the superior advantages of higher material removal rate, lower surface roughness and lower threshold bias voltage. The nanoscale to microscale 2.5D square patterns in the depths of 6–80 nm could be generated on the metallic thin film samples, such as copper and platinum under the coupling effects of mechanical force and electric field. The machining depth and surface roughness is tunable by the distinctive machining parameter settings. The underlying machining mechanisms are attributed to the coupling influences of the electric field induced electric discharge and possible annealing behavior, along with the mechanical force induced surface indentation and scratching.