What is a dungeon? That’s the first question. A dungeon might not necessarily be a dungeon in the classical sense, for instance, a clearing in the woods that is overrun by beasties and evil spirits might be classed as a dungeon. So whether you’re talking about a cottage full of evil spirits, a clearing, a fort, a proper dungeon and so on, as long as it’s its own separate icon on the map, with a few exceptions of course (monuments, major cities (and places within the cities), etc.) you should be able to “clear” it.
But wait, how do you clear it? Well, you basically go in and kill everything in there and grab every unique weapon/item/armour piece that’s found in there. In fact, we think killing stuff is enough actually. It’s that easy. The best thing is, if you bring up the menu, go to map, you’ll be able to see areas you’ve cleared with a “cleared” tag next to it. You’ll get this one as you work through the rest of the trophies, guaranteed. If you want to check your progress, there's a stat in the stats area too.