Use eac3to (to rip/demux) with AnyDVD HD in the background. Eac3to is fantabulous, it; -rips the main movie only (Use AnyDVD's ripper for the whole disc) -fixes gaps/overlaps on seamless branching titles, -converts audio if needed -removes dialogue normalization on AC3 and TrueHD tracks, -and even muxes the video stream to mkv for re-encoding. -detects mpls information (audio/subtitle/chapters and other track information) -plus a tonne of other great stuff. It's a command based application or there are a couple of GUIs available too. I can work with the whole BD sructure as well directly from your PC's HDD.