One way is with VirtualDubMod (http://sourceforge.net/project/showf...group_id=65889
). The subtitles are in the streams list, they can be removed, extracted / disabled.
There's also MKVTools (http://www.videohelp.com/tools/MKVtoolnix
). Compared to VirtualDubMod, MKVTools is updated more recently and has better support of MKV format. I find VDM easier to use, but MKVTools is the better app. It can demux the mkv file into it's individual streams ( including subs ) and remux the parts you want to keep.