This achievement should come through time. As you go to different locations, eliminating all hostiles counts as clearing. This can be caves, giant camps, ruins, etc.
What to look for would be on the World Map; hovering your cursor over a location and seeing if it has a note below the name saying "Cleared".
Also, defeating the final enemy at a site will cause a soft crescendo of music. It's a nice auditory sign to let you know the dungeon is cleared.
Do this 50 times and the achievement is yours.