According to a method for Adaptive Loop Filter (ALF) processing of reconstructed video, multiple indicators are signaled in slice at an encoder side or parsed at a decoder side, where the multiple indicators are Adaptive Parameter Set (APS) indices associated with temporal ALF filter sets for the ALF processing. A current indicator is determined from the multiple indicators, where the current indicator is used to select a current ALF filter set. Filtered-reconstructed pixels are derived for the current block by applying the current ALF filter to the current block. In another method, if the ALF processing applied at a target sample requires an outside sample on other side of a target virtual boundary from the target sample, the outside sample is replaced by a padded sample.