The atomic force microscope (AFM) tip-based nanomechanical machining has been demonstrated to be a powerful tool for fabricating complex 2D∕3D nanostructures. But the machining scale is very small, which holds back this technique severely. How to enlarge the machining scale is always a major concern for the researches. In the present study, a modified AFM tip-based nanomechanical machining system is established through combination of a high precision X-Y stage with the moving range of 100 mm × 100 mm and a commercial AFM in order to enlarge the machining scale. It is found that the tracing property of the AFM system is feasible for large scale machining by controlling the constant normal load. Effects of the machining parameters including the machining direction and the tip geometry on the uniform machined depth with a large scale are evaluated. Consequently, a new tip trace and an increasing load scheme are presented to achieve a uniform machined depth. Finally, a polymer nanoline array with the dimensions of 1 mm × 0.7 mm, the line density of 1000 lines/mm and the average machined depth of 150 nm, and a 20 × 20 polymer square holes array with the scale of 380 μm × 380 μm and the average machined depth of 250 nm are machined successfully. The uniform of the machined depths for all the nanostructures is acceptable. Therefore, it is verified that the AFM tip-based nanomechanical machining method can be used to machine millimeter scale nanostructures.