Recently a new phenomenon was found that the change of liquid crystal alignment for hexagonal columnar (Col(h) ) mesophase is realized under the polarized infrared laser irradiation using an free electron laser (FEL) via the vibrational mode excitation of a chemical bond in the mesogen. For Col(h) mesophase of hexahexyloxytriphenylene (C6OTP), a new domain with a certain uniformity of molecular alignment could be obtained and one can control the director orientation based on the selected combination of the polarization direction of the incidence and the direction of the transition dipole moment for the vibrational excitation. This phenomenon could be observed only for the relatively higher-ordered liquid crystals with the higher viscosity such as Col(h) mesophase not for discotic nematic as well as calamitic nematic and smectic A/C phases, meaning it could be good for the liquid crystalline semiconductors for the fabricating organic devices.