Lyotropic chromonic liquid crystals (LCLCs) have been extensively studied because of the interesting structural characteristics of the linear aggregation of their plank-shaped molecules in aqueous solvents. We report a simple method to control the orientation of LCLCs such as Sunset Yellow (SSY), disodium cromoglycate (DSCG), and DNA by varying pulling speed of the top substrate and temperatures during shear flow induced experiment. Crystallized columns of LCLCs are aligned parallel and perpendicular to the shear direction, at fast and slow pulling speeds of the top substrate, respectively. On the basis of this result, we fabricated an orthogonally patterned film that can be used as an alignment layer for guiding rodlike liquid crystals (LCs) to generate both twisted and planar alignments simultaneously. Our resulting platform can provide a facile method to form multidirectional orientation of soft materials and biomaterials in a process of simple shearing and evaporation, which gives rise to potential patterning applications using LCLCs due to their unique structural characteristics.