How to delete the gameObject with in prefab Instance and then apply by code?

In my case , I want to delete the mousepad01 object from the parent (which is a prefab instance ) by code and then apply it.. Is that possible?

 

You can delete it by creating a new script and then assigning it to the prefab master (the parent that parents everything in the prefab.)
In the script, do this:

Code (CSharp):

1. public void deleteObject(GameObject obj, float wait)
2. {
3.    // Obj: The object that you want to delete
4.    // wait: After how many seconds the object is deleted after
5.    // calling this method
6.    GameObject.Destroy(obj, wait);
7. }

Call this function and you should be fine. I don't understand what you mean by "apply".
Hope this helps!