Anisotropic thin films have been successfully prepared by depositing aminonaphthoquinone dyes under vacuum through evaporation on an oriented poly(tetrafluoroethylene) [PTFE] surface aligned by a friction-transfer technique. Polarized absorption spectra (UV-visible or IR) were employed to investigate the molecular orientation in the films. The results indicate that 2,6-bis(butylamino)-4,8-dihydroxy-1,5-naphthoquinone molecules are oriented with their naphthoquinone (NQ) long axes parallel to the PTFE chains and that they form a strong three dimensional molecular stack through intermolecular hydrogen bonding and pi-pi interactions. The results also indicate that 4,8-bis(p-butylanilino)-1,5-naphthoquinone molecules are oriented with the NQ axes relatively parallel to the PTFE chains and that they turn the axes around to the direction perpendicular to the chains during the polymorphism induced by heat.