Recent findings were briefly described for the liquid crystal alignment change under the polarized infrared laser irradiation using an free electron laser (FEL), which causes the excitation of vibrational mode of chemical bond in the mesogen. For hexagonal columnar (Col(h)) mesophase of hexahexyloxytriphenylene (C6OTP), a new domain with a certain uniformity of molecular alignment could be attained, in which one can control the director orientation in the combination of the polarization direction of the incidence and the direction of the transition dipole moment for the vibrational excitation. This phenomenon is not observed for the relatively lower-ordered liquid crystals with the lower viscosity such as discotic nematic (N-D) phase as well as nematic (N) and smectic A/C (SmA/SmC) phases of calamities, It could be expected that the polarized infrared irradiation gives a novel technique of domain control of the highly viscous mesophase, which is applicable to a fabrication of organic devices by use of liquid crystalline materials for electronics.