The MKV format allows for multiple subtitle streams, include Unicode for closed captioning. You can use the mkvtoolnix to extract from that file just the audio/video/subtitle streams that you want. The command-line structure is somewhat complicated so you'll need to look it up.
However, if you have subtitles burned into the picture, you cannot get rid of those because they are actually part of the video. If you're seeing subtitles on by default and cannot turn them off through the Subtitle menu, then you have burned in subtitles.
The SRT and SUB files ARE the subtitles if you're using AVI files, so all you need to do is delete the files and the subtitles won't appear.
All good video players will also have an option to Enable/Disable subtitles whether they are embedded in the MKV container or as external SRT/SUB files. I recommend Media Player Classic.
Closed captioning? I don't think I've ever come across a video that has both that and subtitles. Maybe the encoder isn't doing that good a job? – Ignacio Vazquez-Abrams – 2011-02-08T01:31:32.550
Very late reply, but here it goes. It's not that the movies have both subtitles and closed captioning. I'm talking about subtitle files which have added lines for things like [EXPLOSION] and other sounds. I wanted to remove these lines from the subtitle file. I'm not a native English speaker so I'm a little fuzzy on the terminology. – Skumberg – 2011-03-16T22:35:20.097