The layers in the controller.
It's important to note that the AnimatorControllerLayer are returned as a copy. The array should be set back into the property when changed.
class ControllerModifier
{
UnityEditor.Animations.AnimatorController controller;
public void ModifyLayers(int layerIndex, string newName)
{
UnityEditor.Animations.AnimatorControllerLayer[] layers = controller.layers;
layers[layerIndex].name = newName;
controller.layers = layers;
}
}