We present new technique for nano-structuring of conducting polymers using femto-second (fs) laser in P3HT:PCBM films with special chain alignment. In an optimized condition of fs laser (1030 nm) irradiation on P3HT:PCBM films, the surface changed into a photoexpanded structure. The crystalline order of edge-on P3HT decreased, while the crystalline order of face-on P3HT increased in the photoexpanded area. The chain alignment of face-on P3HT was affected by the polarization direction of irradiated laser. The PCBM amount also increased in the photoexpanded area in comparison with the pristine area. The results of micro RAMAN measurement confirmed the stability of P3HT chains under the laser irradiation, i.e the main P3TH chains were kept its chain configuration and bonds after laser in photoexpanded areas. These results imply that orientation of P3HT crystals can be selectively controlled into face-on configuration by the fslaser irradiation.