Nanobundles patterns can be formed on the surface of most thermoplastic polymers when the atomic force microscope (AFM)-based nanomechanical machining method is employed to scratch their surfaces. Such patterns are reviewed as three-dimensional sine-wave structures. In the present study, the single-line scratch test is used firstly to study different removal states of the polystyrene (PS) polymer with different molecular weights (MWs). Effects of the scratching direction and the scratching velocity on deformation of the PS film and the state of the removed materials are also investigated. Single-wear box test is then employed to study the possibility of forming bundle structures on PS films with different MWs. The experimental results show that the state between the tip and the sample plays a key role in the nano machining process. If the contact radius between the AFM tip and the polymer surface is larger than the chain end-to-end distance, it is designated as the “cutting” state that means the area of both side ridges is less than the area of the groove and materials are removed. If the contact radius is less than the chain end-to-end distance, it is designated as the “plowing” state that means the area of both side ridges is larger than the area of the groove and no materials are removed at all. For the perfect bundles formation on the PS film, the plowing state is ideal condition for the larger MW polymers because of the chains’ entanglement. SCANNING 35:308-315, 2013. © 2012 Wiley Periodicals, Inc.