There is another option though: let them fight. If vassals do not convert with the player, then there will be an opinion penalty with each vassal who holds a different religion or culture. Just keep in mind that either of these actions can potentially have ramifications.
Players can also opt to convert to the local culture or change their religion. Are they from a different culture? Go to the steward and have him or her attempt to spread the ruler’s culture. Is it because they are of a different religion? Go to the council and have the bishop convert them. Then locate these counties on the map, zoom in, and determine why the ruler's popularity is so low. Click on the faction tab and determine which counties are affiliated with the group.
The main factor rulers want to pay attention to when dealing with these factions is their popularity in certain counties. Both because they tend to have little military power and because getting them to dissolve can be fairly easy. Of those, it is usually the populist and peasant rabble faction types that are easier to deal with. These include peasant rabble, populists, liberty, claimant, and independence factions. The first thing to understand is that there are different types of factions.