Scutes can only be obtained at the moment a baby turtle grows into an adult (the turtle will drop 1 scute as it grows).
5 scutes can be combined to create a turtle shell, a helmet which players can choose to equip. Scutes can also be used to brew potions of the turtle master. Scutes can be used to repair turtle shells on an Anvil. Cleric and leatherworker Villagers have a chance to buy scute in exchange for an Emerald.