I just went through these in the Banning Royals thread, but here are a number of steps to take to get rid of a troublesome Duke:
1. Dissolve his duchy.
2. If he rules a city, stop selling him food and wait for the peasantry to toss him out on his butt. This is inevitable if you can make the food embargo stick.
3. Put a huge bounty on him and/or directly recruit infiltrators to attack him while promising them amnesty if they get caught.
4. In conjunction with stabbings, sick a priest/diplomat on his region to destroy morale and loyalty while he's (hopefully) wounded and hope the peasants toss him out.
5. Get a priest to auto da fe the bastard multiple times until one sticks.
6. Fine him into oblivion.
7. Tax him into oblivion.
8. Give his region away to another realm.
9. Ban him while he's away from his region, wounded, or otherwise unable to secede.
So yeah, those are just a handful of ideas. Get creative. Dukes are not untouchable. If you have enough support, most of the above options should be available to you. If you don't, you've got no business moving against that Duke in the first place.
