The first transformation mask is the Deku Mask. You receive it automatically once you've completed the first three days. On the last days, pay Skull Kid a visit in the Clock Tower. Consequently after your chit-chat with Skull Kid, a mini-battle is about to happen. It's fairly easy, though. Simply blow the Ocarina who he's holding out of his hand, grab the Ocarina and play the Song Of Time. You'll warp back to the first day, pay a visit to the Happy Masks Salesman and you'll receive the Deku Mask subsequently.
As for the second transformation mask, that's the Goron Mask. It's
obtained by talking to the owl in Goron Village. Follow him to the secret shrine which contains the Lens Of Truth. Consequently, when you've obtained the Lens Of Truth, return to the place where you met the owl.
There you shall meet a Goron Ghost, namely Darmani. Who used to be the Goron Elder of the village. Warning, you need to activate your lens of truth to be able to see it. Afterwards, you'll have to follow him to the Goron Graveyard. When you've reached the Graveyard, play the Song Of Healing and let the Goron rest in peace. Hence he'll give you the Goron Mask!
After you beat the Snowhead temple, head for Great bay Coast. Once you have arrived, you'll notice a Zora lying in the water. Obviously, it's the guitar player from the Indigo-go's band. You'll need to 'grab' him and take him back to the shore. He will tell you his story, then you'll receive the Zora Mask afterwards.
- NOTE: This is just a small part.