So Mote It Be

Means "so be it" or "so may it be" and is used after Masonic Prayers.  Sometimes, "Amen, So Mote It Be" is used after a prayer or other occasion calling for its use.

I have only ever heard this term used by Freemasons, so it seems to be purely Masonic.

This seems to be used as a substitute to the word 'Amen' for whatever reason it was chosen.