In order to construct an intelligent functional nano-interface, the self-organized structure of Langmuir-Blodgett (LB) film was investigated by atomic force microscopy (AFM). As a building block, a monodisperse loop-helix-helix triblock copolypeptide containing the helix of which hydrophobic L-leucine residues align on a single face, “leucine zipper”, was synthesized by recombinant DNA techniques with a designed amino acid sequence. AFM observation on the surface structure of LB films constructed at surface pressures of 2, 5 and 18 mN/m revealed that structural transition from ring- or disk-like aggregations to a lane-like fabrication occurred with compression of the copolypeptide membrane on the water of pH 4. The leucine zipper in the copolypeptide was suggested to perform as an important basis for nanostructure formation through a hydrophobic interaction. Exploitation of the recognition and specific binding sites in the copolypeptide will allow the self-assembling mechanism of the copolypeptide to be developed to a novel nano-template.