Fine structures provide materials with various functionalities such as friction reduction and water repellency. A short-pulsed laser is a suitable method to effectively fabricate fine structures through self-organization, called as LIPSS (laser induced periodic structures). However, this method has difficulty in control of LIPSS since the principles and the phenomena have not been clarified completely. It has been reported that LIPSS follow debris on a material surface, hence, the short-pulsed laser assisted by mechanical processing was proposed, and the straightness and the aspect ratio of LIPSS were improved by laser irradiation on the surface with the straight microgooves. The short-pulsed laser assisted by mechanical processing was developed to control LIPSS and fabricate zigzag LIPSS, and the effects of the surface geometry before laser irradiation on LIPSS were investigated. Firstly, laser irradiation was conducted on the microgrooved surfaces with changing the angle of laser polarization to investigate the effects of the angle between groove direction and laser polarization on LIPSS. When the angle were from 45° to 90°, LIPSS followed the microgrooves regardless of the laser polarization. Based on the results, the laser was irradiated on the surfaces with zigzag microgrooves created by ultraprecision cutting, and zigzag LIPSS were fabricated as following zigzag microgrooves under the proper conditions. This study demonstrated the importance of the initial surface shape and the effectiveness of the short-pulsed laser assisted by mechanical machining to control LIPSS freely since the surface plasma waves are propagated from unevenness on the material surface.