Methods and apparatus of processing omnidirectional images are disclosed. According to one method, a current set of omnidirectional images converted from each spherical image in a 360-degree panoramic video sequence using a selected projection format is received, where the selected projection format belongs to a projection format group comprising a cubicface format, and the current set of omnidirectional images with the cubicface format consists of six cubic faces. If the selected projection format corresponds to the cubicface format, one or more mapping syntax elements to map the current set of omnidirectional images into a current cubemap image are signaled. The coded data are then provided in a bitstream including said one or more mapping syntax elements for the current set of omnidirectional images.