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VLC is rendering it as 2 views side by side going on at the same time.
The MKV format is actually an archive container like a TAR, ZIP or RAR container. There could be one, two or hundreds of audio/videos within the container. Search engine nomenclature for a ZIP file would be "How extract Zip file"
I'd go for mkvtoolnix also. You should have 2 video streams in your mkv file, both of them may be declared as 'default'. You may just have to withdraw this 'default' attribute from one of these streams.
If you place a cardboard vertically along the dividing line between two views, and use your nosetip to hold the cardboard in place, the two views will probably melt together into one. It may spread out depthwise, though.
You might even like it. First time I saw a 3D image pair in a book on photography and tried with the cardboard, I had the greatest Wow! experience I ever have had from a book!