A method and apparatus for Intra prediction coding in multi-view video coding, three-dimensional video coding, or screen content video coding are disclosed. A first filtering-disable-flag associated with a high-level video data is determined to indicate whether to disable at least one filter from a filter group. If the first filtering-disable-flag is asserted, one or more selected Intra prediction modes from an Intra prediction mode group is determined, and at least one filter from the filter group for the current block is skipped if the current Intra prediction mode of the current block belongs to the selected Intra prediction modes. The system may further determine a second filtering-disable-flag associated with a low-level video data corresponding to a current block level or a higher level than the current block level to disable said at least one filter from a filter group for the low-level video data.