Does anyone know how to export a emd file with milkshape?
This isn't really the place to ask this. Try the help file, or the MilkShape website.
http://www.swissquake.ch/chumbalum-soft/
If I'm correct you want to use the Character3D plugin, why else would someone try to export an .emd file... If this is the case you can also use the .ms3d format for Char3D, which is the normal Save-format for Milkshape.
But to answer your question; No, milkshape can't export an .emd file.