Using MKVtoolnix or similar Matroska tools it should be easy enough to convert videos in MKV format to MKV3D format.
Convert Matroska multimedia container to Matroska 3D video format file.
We have found 3 software records in our database eligible for .mkv to .mkv3d file format conversion.
Microsoft Windows software - convert mkv to mkv3d on Windows
A program for working with Matroska MKV files
Convert from mkv file format
The tables with software actions are a good pointer for what a certain program does with various file types and often may give users a good hint how to perform certain file conversion, for example the above-mentioned mkv to mkv3d. However, it is not perfect and sometimes can show results which are not really usable because of how certain programs work with files and the possible conversion is thus actually not possible at all.
Apple macOS / Mac OS X software - convert mkv to mkv3d on OS X
A Mac version of the video editing suite for Matroska
Linux/Unix software - convert mkv to mkv3d on Linux
A set of utilities for handling Matroska files in version for Linux