Peter (Pollys13) has been asking about this for the spindle and with a tenoner.
I must admit I forgotten about using a router to do them, but the way I used to do it was to make a jig using a piece of MDF cut to about 600mm long and the width of the rail plus 80mm and then screw two bits of wood the thickness of the rail and 40mm wide along the 600mm length to it spaced apart the width of the rail.
Then I would put the scribe cutter in the a hand held router, then put the rail in the u shape of the jig and clamp, then screw another piece of wood into the 40mm wide pieces this would be set so when the base of the router ran along it the scribe cutter it would cut the scribe in the correct place on the shoulder of the tenon.
It is a bit of a fiddle to set up the first time but once you have got the setting right will give repeatable joints.