One-dimensional nanostructures are ideal building blocks for functional nanoscale assembly. Peptide based nanofibers have great potential in building smart hierarchical structures due to their tunable structures at the single residue level and their ability to reconfigure themselves in response to environmental stimuli. Recently we observed that silk-elastin based protein polymers (SELP) self-assemble into nanofibers through conformational changes on a mica substrate. In addition, we demonstrated that the rate of self-assembly was significantly enhanced by applying a nanomechanical stimulus using a tapping mode atomic force microscopy (AFM). The orientation of the newly grown nanofibers was mostly perpendicular to the scanning direction, implying that the new nanofiber assembly was locally activated with directional control. Furthermore, controlling tapping frequency and density of tapping showed that repetitive tapping is crucial to create nucleation areas, hence nanofiber growth. The similar self-assembly of SELP nanofiber was also induced in a lateral force mode of AFM. Lateral force profiles show a significant correlation between frictional force and nucleation formation, indicating that strong interaction between SELP and AFM tip is a prerequisite for nucleation formation. Underlying molecular mechanisms are proposed based upon the characteristics of the friction force profiles, nucleation areas and their growth behaviors observed in time lapse AFM images. Finally mechanically guided nanofiber patterns were successfully created on a mica substrate using this technique.