Instantiating prefab question.

If I instantiated a prefab twice in my scene. So basically I have two clones of my prefab. Is there a way I can differentiate between them through script? If yes, how?

To be more clear, I am raycasting two rays. I want to be able to tell if both rays hit the same clone, or if each hit a different clone.

You can give them each a unique name, or add some sort of ID property in one of the attached scripts and set the ID to a unique value.