Manipulate a gameobject on runtime and clone it with the current shape

I'm making an application that allows a user to build and manipulate objects. One of the features concern changing the shape of an object say a cube, and then clone this exact cube with it's new shape as many times as one might need. I'm unsure what to do exactly since I don't think I can use prefabs for this task as the shape or rotation will likely change each time and the basic object needs to remain intact. Is it possible to create new objects and add components with the changed values? If so does anyone have any links or ideas how - I can't seem to find any. Thanks