As Raruu told you, in order to make it to the top of Ganon’s Tower you must bring down the six barriers.
Starting with the Green Barrier, the first one to your right, and working our way around. When you get to the back end of each room use a light arrow and shoot it straight through the golden orb surrounded by the barrier.
Green – (Forest)
Start by killing the wolf in the first room and gaining your five rupees out of the chest. Then use either Din’s Fire or Fire Arrows to light up the four torches. The fifth torch is above the door.
The next room is just a matter of using your Hover Boots and Longshot to get around. When you get stuck in the middle of the room use your Longshot to grapple back to the start of the room. For the rupee that appears to be to high, there is a switch on one of the lower platforms you can use to make a stand appear under the rupee.
Blue – (Water)
In the first room kill both of the two enemies. Then take some of the blue fire and use it to burn away the red barrier guarding the now unlocked door.
Make sure you take some Blue Fire into the second room. We’re going to assume the door you enter from is south. Push the block furthest away from you east, then south into the hole. Then push the second block east, north and then west into the crevasse in the wall. Now climb that block, use the blue fire and pound the switch using your Megaton Hammer.
Purple – (Shadow)
Use your Fire Arrows to light up the torch on the right side of the room, and then run across the platforms that appear. When you get to the platform with nothing on it but the black square turn on your Lens of Truth. Then walk the platform that goes off to the right, not the one that goes straight to the door. Hit the switch at the end of that path then go towards the door
One other thing in this room that you must do: The platform that has the black square on it, go there. Then light up the torch to the left of the door at the end of the room. A platform will appear leading you to a switch on the lower right side of the platform. Go down and press it and open the chest to receive the Golden Gauntlets.
Red – (Fire)
Go around the room collecting the silver rupees. One of them is under that huge grey block. Walk up to it, and with your new Golden Gauntlets, you will be able to pick it up and throw it.
Orange – (Spirit)
For the first room I suggest you start by taking out the Beamos, then start collecting the rupees. For the ones that have spikes that move to fast or are to close to the rupees just move the statues out further and the spikes will take longer to go across. For the rupee that’s elevated to high to reach just use you Longshot on the target above it.
Say hello to the first room in the game that actually lets you make good use of the Bombchu. Hope you have some. Look to the roof for a hole, and when you find it, launch a Bombchu through it. It should hit the crystal on the other side if aimed correctly. The door will then open.
In this last room look to the roof again. Shoot a Fire Arrow at the cobwebs and the sun will shine through, and then light up each sun picture until you find the one that opens the door.
Yellow – (Light)
The last room is the Light Barrier. You have to pick up and throw away the block guarding its entrance. Kill all the enemies in the first room by turning on the Lens of Truth to see them. One Skulltula and three bats. Use the key to gain entrance to the next room.
Play Zelda’s Lullaby on the triforce to drop a chest with a key in it for the second door.
Collect all silver rupees in this room to open the door.
As I’m sure you’ve noticed, the object creating the barrier is not here. By turning on the Lens of Truth you will reveal that there is a hidden section behind this pedestal that leads to the real one, where you can take out the barrier.
I recommend you complete this quest first:
Now you can continue to Ganondorf.
