The percentage explored is displayed under each area on the map screen. The secrets found or collectibles obtained will not matter. Visit 100% in all areas to get the "Master Of The Forest" achievement. Map sections that are unexplored appear darkened at the map screen. Note: Certain areas are only accessible by finding secrets. Also, explore the boundaries between map areas to make sure they are counted as explored. Be careful, as you cannot return to the following areas to fully explore after the listed progression:

Mount Horu: Once entered, you cannot return to any other part of the map.
Ginso Tree: You cannot return after freeing the waters.
Misty Woods: You cannot return after removing the veil of darkness.
Forlorn Ruins: You cannot return after freeing the wind.

Additionally, some of those areas have two paths that take you to the same point. Thus, you must return and take the other path.