Boss Challenge
The Boss Challenge is an additional mode that was added in the Nintendo 3DS release of Ocarina of Time 3D. The Boss Challenge is available in both the regular version, as well as the Master Quest version of the game, with there being notable difficulty changes between the two versions.
Accessing the Boss Challenge
After Link has have completed the Forest Temple and returned to the Temple of Time, he will find Sheik waiting for him. After speaking to him, he mentions that Link can now return to his tree house in Kokiri Forest and relive boss battles from the past. At this point Link can return and examine his bed, and he'll have the option to revisit these boss battles. At that moment, Link can battle with Queen Gohma, King Dodongo, Barinade, and Phantom Ganon. The remaining bosses will become available as Link completes those respective dungeons.
Restrictions
When Link faces off with some of the bosses, he will be restricted in terms of the number of heart containers he has, the items he current carries, as well as any recovery items that he has in bottles.
Master Quest
In the Master Quest version of the Boss Challenege , Link does not get any recovery items at all. Furthermore, Link only has 3 hearts in Master Quest for the child bosses, and only has 5 hearts for the adult bosses.