Methods and apparatus relating to encoding and decoding stereoscopic (3D) image data, e.g., left and right eye images, are described. Various pre-encoding and post-decoding operations are described in conjunction with difference based encoding and decoding techniques. In some embodiments left and right eye image data is subject to scaling, transform operation(s) and cropping prior to encoding. In addition, in some embodiments decoded left and right eye image data is subject to scaling, transform operations(s) and filling operations prior to being output to a display device. Transform information and/or scaling information may be included in a bitstream communicating encoded left and right eye images. The amount of scaling can be the same for an entire scene and/or program.