We researched properties of lyotropic liquid crystals when they are aligned in the lines of a high aspect ratio which is fabricated by secondary sputtering lithography. Lyotropic chromonic liquid crystals behave like a stacked rod due to the π-π interaction of the core which allows molecule to form a highly ordered state. Aligned state is verified by polarized optical microscope and a phase diagram of the material shows that transition temperature between nematic phase and isotropic phase shows increment as the concentration of the material increases. The anchoring energy which is calculated by Berreman’s theory with elastic constant of materials is also shown in the graph. Lyotropic chromonic liquid crystals are the very promising materials having polarizing property which is applicable to displays, optoelectronic devices and biosensors.