Conductive atomic force microscopy (CAFM) nanolithography was utilized to modify a silicon surface. With this method generating the silicon oxide relief by CAFM, liquid crystal (LC) alignment is under a good control in the micron or submicron region. It establishes high-resolution images with a pixel of a smaller size. Compared with the conventional cloth rubbing and AFM scratching techniques, the CAFM nanolithography prevents scratching damage, dust contamination and residual static electricity problems. Furthermore, this inorganic alignment method can also avoid the damage from UV light exposure and high-temperature environment.