Instantiate - Instancing a prefab

I just started learning Unity and Javascript, and there is one thing I cant seem to grasp.
I tried reading all the online information, but I just need someone to put i plainly.

I have a gameobject prefab Box. I wrote a script that makes an instance of that Box prefab every second. In a few seconds I have a bunch of boxes in my floor.

How do I reference a single instanced box from that bunch?

Say I want to destroy Box that spawned 6th?

How would I reference that particular instance of the prefab?

Thanks!

so it would be basically

yourBoxes[5].bounceUpAndDown();
yourBoxes[5].spinAround();
Destroy( yourBoxes[5] );

or whatever you need.