The current software for creating and editing animation offers the possibility of dividing variable objects into layers. This paper suggests a method to render and edit each of right and left layer in the process of creating a 3D stereoscopic animation. It is possible to apply a variety of effects to left and right images and to adjust the gap of binocular parallax through this method so that wider variation of images and richer sense of depth can be produced. In addition, this method offers freedom of deleting and inserting an object, controlling size and position of the object and adjusting the gap of binocular parallax. Thus, new sense of depth can be obtained. This method shows the results to apply various effects on the 3D stereoscopic image and to reduce visual fatigue rather than the method to render simultaneously both of left and right layer.