...from a file folder

[Mengistuh1]

Make MKV really needs to be able to make MKV files from a file/file folder that is directly on the computer itself, in addition to being able to read from the disk; this would make it more versatile and desirable.

[Woodstock]

Are you saying that Open->Files isn't working?

[Grauhaar]

Open-> File needs the "index.bdmv" (Blu-ray) or the IFO files (DVD) to get the needed Meta data to create the mkv file.

If you want to put normal video and audio files into an MKV container you can do this with "MKVToollNIX" and specify the Meta data in the settings.