We demonstrated the capillary force lithography (CFL) method for controlling the azimuthal anchoring energy of a liquid crystal (LC) alignment layer. When a thermoplastic polymer film is heated to over the glass transition temperature, the melted polymer is filled into the mold structure by the capillary action and the aspect ratio of the pattern is determined by the dewetting time of the CFL process. Here, the proposed method showed that the azimuthal anchoring energy of the LC alignment layer could be simply controlled by the surface relief patterns which were determined by the dewetting times during the CFL patterning.