Whisker-type poly(3-hexylthiophene-2,5-diyl) (P3HT) nanofibers were aligned by restricting their growth direction using an approximately 100–1000 nm wide narrow groove fabricated by thermal nanoimprinting. In grooves made of an amorphous fluoropolymer (CYTOP™) with widths of less than 1500 nm, the nanofibers oriented uniaxially perpendicular to the groove and their length was limited to the width of the groove. This result indicates that the nucleation of nanofibers tends to be selectively promoted near the interface of CYTOP™ with fluoro-groups, and nanofiber growth perpendicular to the wall is promoted because P3HT molecules are supplied more frequently from the center of the groove. Furthermore, the orientation induced anisotropic conductivity, and the conductivity parallel to the oriented nanofibers was more than an order of magnitude higher than that perpendicular to the oriented nanofibers.