Complex 1, synthesized from anionic shortened single-walled carbon nanotubes and cationic ammonium lipid dissolved in organic solvents, is cast on pretreated transparent flexible poly(ethylene terephthalate) (PET) films under a higher relative humidity to form thin films with self-organized honeycomb structures. The cell sizes are controllable by changing the experimental conditions. The lipid, which is the cationic part of complex 1, is easily removed by a simple ion-exchange method, while maintaining the basic honeycomb structures. After the ion exchange, the nanotube honeycomb films on PET with thinner skeletons exhibit a dramatic decrease in the surface resistivity from insulating to conducting. Carbon nanotubes with honeycomb structures formed by the self-organization on flexible polymer films are useful in many areas of nanoscience and technology including nanomaterials, nanoelectronics, nanodevices, catalysts, sensors, and so on.