Saving Clone Prefabs

I have a script to save location on a transform but it saves in player prefs my problem is that when i place down clones of objects with my building script they all have the same prefs name and all load to the same spot when i load, I want to know is there any way that i can save all the clones under an empty gameobject and then save that gmeobject as a prefab so it keeps all the clones is the same location and then load that single prefab back into the game with all the clones inside the prefab? or do you have some easier way of saving all the clones seperately?

Do you really need to destroy all the clones or would it be easyer to use the .SetActive(false) method for all the clones and save the list as an array to reactivate them?