Minimization of visual fatigue is important for production of high quality stereoscopic 3D contents. Vertical disparity of stereo images occurred during contents production is considered as the main factor of visual fatigue. To ensure correct stereoscopy vertical disparity needs to be eliminated. In this paper, a method for automated image alignment was proposed for Stereoscopic 3D contents generation and post-processing steps. The proposed method consists of two parts: rectification for image alignment and camera motion detection. The proposed method showed that its rectification performance was the most superior among the existing methods tested and that camera motion detection had a success rate of 98.35%. Through these evaluations, we confirmed that the proposed method can be effectively applied to 3D contents production.