You can convert MKV3D videos to MKV using MKVtoolnix program. The resulting format will however loose the 3D stereoscopic aspect.
Convert Matroska 3D video format file to Matroska multimedia container.
We have found 3 software records in our database eligible for .mkv3d to .mkv file format conversion.
Microsoft Windows software - convert mkv3d to mkv on Windows
A program for working with Matroska MKV files
Convert from mkv3d 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 mkv3d to mkv. 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 mkv3d to mkv on OS X
A Mac version of the video editing suite for Matroska
Linux/Unix software - convert mkv3d to mkv on Linux
A set of utilities for handling Matroska files in version for Linux