You can convert mk3d to mkv, i.e. Matroska MKV 3D files (.mk3d) to normal Matroska MKVs (.mkv) with any dedicated Matroska software like MKVtoolnix or similar. Simple file extension renaming is not sufficient, considering both formats are different.
Open MK3D file Open MKV fileA set of utilities for handling Matroska files in version for Linux
A Mac version of the video editing suite for Matroska