Recently, machining centers have been actively adopting high-speed positioning systems to enhance operational efficiency and productivity. This study focuses on applying input shaping techniques to a machining center to improve the machining precision. Simulations were performed using a minimal impulse input shaper on a two-axis stage, considering its anisotropic characteristics. A comparative analysis was performed to assess the effectiveness of input shaping by varying the material, feed rate, reduction ratio, and depth of cut. The machined specimens were measured using a digital microscope, surface roughness tester, and an image dimension measurement device. Successful experiments were conducted to demonstrate the improved processing quality of the machining center during combined linear and circular cutting processes. Both the simulations and experiments confirmed the significant effectiveness of the proposed method in enhancing the machining precision of the machining center.