Fluorinated polyimides have very low surface energy and influence the liquid crystals effectively to reduce the surface energy. Fluorines can be introduced to the main and side chains, and the fluorine contents and interfacial orientation can be important factor to control the surface energy. We synthesized two polyimides fluorinated at main chains and side chains. The surface energy was modified with variation of blending ratios of the fluorinated polyimides with 1,2,3,4-cyclobutanetetracaroxylic dianhydride (CBDA)/3,5-diaminobenzyl alcohol (DBA). The LC cells were fabricated after treating the polyimide surfaces. Polarized optical microscopy and UV-visible spectroscopy were used to confirm direction of alignment. With the polyimide containing fluorine at the main chain, we could not align LC due to phase separation of surface. However, the polyimide with fluorine at the side chain provided homeotropic LC alignment with very small tilt angle.