In this study, we investigated the effect of surface nano-modification of aromatic fluorinated polyimide (6FDA-6FAP) derived from 2,2'-bis (3,4-dicarboxyphenyl) hexafluoropropane dianhydride (6FDA) and 2,2'-bis (4-aminophenyl) hexafluoropropane (6FAP) on the interaction with proteins and cells. The surface of 6FDA-6FAP was modified by surface-rubbing showed nano-ordered stripes along the rubbing direction. The rat fibroblast FR cells formed multicellular spheroids with high cell density on the rubbed surface then expressed excellent collagen production similarly in vivo, while on the non-modified surface the cells formed two-dimensional monolayers and the collagen production was negligible. The modulation of cell function by the surface nano-modification along with surface micro-modification may be one of the most important considerations during the design and manufacture of novel biochips or tissue engineering materials.