Methods and apparatus of processing 360-degree virtual reality (VR360) pictures are disclosed. A target reconstructed VR picture in a reconstructed VR picture sequence is divided into multiple processing units and whether a target processing unit contains any discontinuous edge corresponding to a face boundary in the target reconstructed VR picture is determined. If the target processing unit contains any discontinuous edge: the target processing unit is split into two or more sub-processing units along the discontinuous edges; and NN processing is applied to each of the sub-processing units to generate a filtered processing unit. If the target processing unit contains no discontinuous edge, the NN processing is applied to the target processing unit to generate the filtered processing unit. A method and apparatus for CNN training process are also disclosed. The input reconstructed VR pictures and original pictures are divided into sub-frames along discontinuous boundaries for the training process.