There's nothing that can be done now to improve the shell. When the tortoise was very young it wasn't kept/fed properly and grew like that. But, as you can see around the lower parts, it has been growing normally for a very long time.
All a tortoise needs is good husbandry, the right food served with variety, clean water and sun shine.
Basically it is from how it was cared for when it was little. Food has a little bit to do with it, but the tortoise's environment was the big kicker. He wasn't set up in a proper habitat.