A method and apparatus for processing in-loop reconstructed video using an in-loop filter is disclosed. In the recent HEVC development, adaptive loop filtering (ALF) is being adopted to process in-loop reconstruction video data, where ALF can be selectively turned ON or OFF for each block in a frame or a slice. An advanced ALF is disclosed later that allows a choice of multiple filter sets that can be applied to the reconstructed video data adaptively. In the present disclosure, pixels of the in-loop reconstructed video data are divided into a plurality of to-be-filtered regions, and an in-loop filter from a filter set is determined for each to-be-filtered region based on a rate-distortion optimization procedure. According to one embodiment of the present invention, computation of cost function associated with the rate-distortion optimization procedure is related to correlation values associated with original video data and the in-loop reconstructed video data. Furthermore, the correlation values can be shared by the multiple candidate filters during the rate-distortion optimization procedure for said each to-be-filtered region. In another embodiment, the correlation values can be shared by multiple candidate to-be-filtered regions of an area of the in-loop reconstructed video data during the rate-distortion optimization procedure for the area of the in-loop reconstructed video data.