The present study demonstrates that surface reformation in polydimethylsiloxane can be controlled using ion-beam (IB) irradiation. This can be done by simply varying the IB incidence angle and requires no change in the energy source. By controlling the incidence angle of IB irradiation, we were able to continuously control the pattern of the wrinkle structure, that is, a randomly formed pattern or an anisotropic one. Moreover, the directional characteristics of the wrinkle pattern control the alignment of liquid crystal molecules. This control is a function of the incidence angle of the IB. These simple methods can provide considerable flexibility in the fabrication of wrinkle structures.