Both MKV and MK3D are the same Matroska container, albeit used for different purposes. A .mk3d file is meant to contain 3D video, whilst .mkv files are the "normal" Matroska Videos. You probably cannot just convert one to another, because 3D movies needs to be recorded that way and cannot be just created from normal ones.
Convert Matroska multimedia container to Matroska MKV 3D stereoscopic video file.
We found 3 software records in the database related to .mkv to .mk3d file format conversion.
Microsoft Windows software - convert mkv to mk3d 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 mk3d. 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 mk3d on OS X
A Mac version of the video editing suite for Matroska
Linux/Unix software - convert mkv to mk3d on Linux
A set of utilities for handling Matroska files in version for Linux