sometimes have I come across MKV files that have built-in subtitles.
Although it’s nice that matroska has that ability, those subtitles are sometimes a nuisance.
They are either in an unwanted language or become hardcoded when you try to convert the video with some app.
Removing them is actually quite easy.
1. Removing built-in subtitles from MKV
First you need a small app called MKVmergeGUI (select the OS you are using).
You load your MKV video by clicking Add.
Then you deselect subtitle track (S_TEXT/UTF8).
Then click Start Muxing.
In a couple of minutes you have a MKV video without subtitles.
2. Extracting built-in subtitles from MKV
For this you need to use MKVextractGUI-2.
Load your video in Input.
Select subtitle track (S_TEXT/UTF8) in Content.
Click Extract.
In under a minute you will have .srt subtitle from that video.
These subs will work with MKV video if you removed them as stated in 1.
http://img651.imageshack.us/img651/833/extractp.jpg