Great Fairy Mask
The Great Fairy Mask is an essential tool for tracking down every fairy in the game. The mask is found in North Clock Town -- you must return the lost fairy to the Great Fairy Fountain after you get the Deku Mask. This mask attracts stray fairies in the dungeons, and it will start glowing when you are close to fairy. Since the fairies are often hidden, the Great Fairy Mask greatly simplifies the process of hunting them down.
Dungeon Preparation
There are four separate dungeons in "Majora's Mask," and each has 15 stray fairies. The four temples are the Great Bay Temple, Woodfall Temple, Snowhead Temple and the Stone Tower Temple. Netting them all on your first run through the temples isn't an easy feat. First, play through the dungeon to get a feel for the layout and the enemies. On your next run-through, get your equipment set and focus on the fairies -- you'll need the Great Fairy Mask, at least three empty bottles and one bottle of green potion (for magic renewal).
Discovering Fairies
The 60 stray fairies within the different temples are often hidden, although you'll occasionally find them floating around in the air. Be sure to look around and use your Great Fairy Mask frequently. For the hidden fairies, the best strategy is to scour the maps room by room, looking for chests, pots and bubbles where they could be hiding. Open every chest you see until you've found all 15 strays. Pay careful attention to out-of-reach objects that require the use of equipment like the Hookshot or Deku Launcher to access -- these objects and areas often house fairies.
Fairy Fountains
Once you've collected the stray fairies in a given temple, you have one more job to do. You must deposit them in their respective Great Fairy Fountains. For the Woodfall Temple fountain, return to the ledge where you played the Sonata of Awakening and use the Deku Launcher to fly to the cave in the distance. For the Great Bay Temple fountain, travel to the Great Bay Coast and swim to the island with palm trees. Hookshot across the island chain and bomb the boulder at the end. Access the fountain for the Stone Tower Temple by jumping into the ravine in Ikana Canyon and swimming to the cave at the extreme right. The Snowhead Temple fountain is found on the way to the dungeon itself; it's inside the large cave you'll see on the way to the summit.