I need convert same mkv file to my ipod lately，and found "AVAide Video Converter", nice，It can support almost all formats of video, such-and-such soft, i hope share it with you，this is tutorial.
1.Choose target format，eg. convert to RM fomat， form AVAide Video Converter's main interface click "TO RM".(eg.image）
2.Click the button Add File at the bottom left of the software interface to add documents you want to convert. AVAide Video Converter supports batch convertion. When you convert several video file, just add several source file is ok, and the software itself will finish the batch convertion task.
3.click "Start Convert" button ，AVAide Video Converter start work，this process very ease，your can click "open the preview window" realtime preview 。
4,With the integrated video player, you can convert only the outstanding part of the video by setting up the start time and end time after preview.
Supplement:
If you want to convert only the outstanding part, first click on the "Play" button and drag the progress bar to the start point of the outstanding part, then click button B and drag the progress bar to the end of the part, click button E and stop playing. Lastly click the "Convert" button.
You also can convert the video file to MPEG, MP4, MKV, 3GP, MOV, WMV, FLV,AVI,DVD format, the method is the same to rm convertion format.
if you want use this soft，donwnload form this website, video convert: http://www.avaide.com/video-converter.html