Hello!
By layer did you mean the sorting layer? If so, you can change the sorting layer and the sorting order from the SortingGroup component of your character prefab.
If you meant layer as in layer (the one at the top of the inspector), then you can change the layer of your saved prefab from the inspector. Apply it to all its children, then make sure to disable InitializeOnAwake on your prefab, so that the layer setting won't get overridden when you run the game.