Power converter devices require a high level of quality because they have a high direct connection with vehicle operation. Therefore, structural bonding was carried out by friction stir welding with excellent mechanical properties. Friction stir welding can cause structural deflection depending on the load of the welding tool, so it is important to control this for high quality flatness. In this study, pre-welding was performed before welding to minimize deflection generated during welding. And deflection reduction data according to the location of pre-welding were analyzed through dynamic analysis. As a result, based on computerized data rather than experimental data an optimized position of pre-welding was secured to minimize the deflection that occurs during friction stir welding. Through this, a process guide that enables high quality structural bonding was presented.