Methods and apparatus for loop-filter processing of reconstructed video are disclosed. According to this method, if a loop-filter is disallowed for a target boundary, the target loop filter is disabled at top, bottom, left and right of the target boundary. According to another method, CC-ALF (cross-component adaptive loop filter) shape is changed across a virtual boundary. According to yet another method, CC-ALF and luma ALF handle unavailable samples in a same way.