Delete children of Instantiated object

When you instantiate, a prefab - it will instantiate the way it's been designed. After the instantiation though, you can alter it, like remove the childs that you don't want it to have. I would probably create a complex type, attach it to the prefab, and based on the values perform certain operations. I would also avoid instantiating and destroying stuff if there is alot of it because it affects the performance, because each time you instantiate something, the memory is allocated to the heap, which eventually keeps growing until you run out of memory. There are object pools that you can use which will greatly improve the performance. (Object pools re-use objects)

Try this

  GameObject copy = Instantiate (prefab, transform.position, transform.rotation)as GameObject;
             for (int i = 0; i <copy.transform.childCount; i++)
             {
                 Destroy (copy.transform.GetChild(i).gameObject);
             }

If it happens a lot you might better off creating seperate prefabs for each object and child objects while linking them through a dictionary inside a scriptable object probably. Then create a custom Instatiate method with the option (parametere) to instatiate the children too or not.

@kaplica the chances of running out of memory in this senario are equal with just instatiating single objects without the child objects, the memory occupied by the child objects will be released as soon they are destroyed, of course will effect negatively the performance.