Step 1 is improve your reputation with the Pope to perfect, either by giving him money via diplomacy or territories, map information, etc.

Step 2 is select your target Catholic nation and attack them.

Step 3 is to watch for Papal warnings. If your relations are perfect you won't be warned with excommunication, only with a lower reputation with the Pope.

Step 4 is to restore your reputation with the Pope after he knocks it down. Give him all the same stuff as before until you're back to perfect.

Step 5 is smash the rest of the world.

The only problem with removing the Pope via armies is that your public order goes down due to excommunication and being at war with the Papacy. You can't get back to being at peace until a new Pope spawns, and if you're especially unlucky he'll ask some far away land for a new home and set up the new Papacy in Dublin, thus making it harder to get peace or kill him again.