Atomic Force Microscope (AFM) has become a popular experimental tool for the nanotribological studies. Nanobundles formation perpendicular to the scanning direction has been reported as a typical wear mode for the thermoplastics, and such bundle structures are also considered as sinusoidal wave micro/nanostructures now. In the present study, the AFM tip based nanomechanical machining method is employed to scratch a polymer Polycarbonate (PC) surface for only once with the normal load of several micro-Newtons in order to achieve the perfect regular nanobundle structures. Based on a modified AFM system, effects of different tip traces in the tip scanning mode and in the sample scanning mode on nanobundles formation on the PC surface are studied. The experimental results show that the controlled reciprocal movement of the stage in the sample scanning mode is feasible for perfect nanobundle structures formation. Moreover, effects of the normal load and the feed on bundles formation in the sample scanning mode are analyzed. Experimental results reveal that the feed value directly affects the formed patterns including the bundles and grooves structures. The reciprocal effect of the tip trace is the decisive factor of forming ideal nanobundles. The repeating times on the same area acted by the tip which are larger than twice are necessary to form a perfect nanobundle structure. (C) 2012 Elsevier B. V. All rights reserved.