Unity Editor Script, put a prefab in editor window, select a transform in Hierarchy, then click Replace button, the tranform will replace with the prefab.

ReplacePrefab.cs

using UnityEngine;
using UnityEditor;
public class ReplacePrefab : EditorWindow {

    [MenuItem("GameEditor/ReplacePrefab")]
    public static void ShowWindow()
    {
        EditorWindow.GetWindow(typeof(ReplacePrefab));
    }
 
	static public GameObject source;
	
    public void OnGUI()
    {
        if (GUILayout.Button("Replace the selected GameObjects with your prefab"))
        {
            ReplaceSelected();
        }
		
		EditorGUILayout.BeginHorizontal();
        source = EditorGUILayout.ObjectField("Prefab", source, typeof(GameObject), true) as GameObject;
        EditorGUILayout.EndHorizontal();

        if (GUILayout.Button("Rename delete (clone)"))
        {
            Rename();
        }
    }
    private static void ReplaceSelected()
    {
        GameObject[] go = Selection.gameObjects;
        int go_count = 0;
        foreach (GameObject g in go)
        {
            go_count++;
			Transform trans = g.transform;
			Transform parent = trans.parent;
			
			GameObject instance = Instantiate(source) as GameObject;
            instance.transform.parent = parent;
            instance.transform.localPosition = trans.localPosition;
            instance.transform.localRotation = trans.localRotation;
            instance.transform.localScale = trans.localScale;

			GameObject.DestroyImmediate(g);
			string name = instance.name;
			instance.name = name.Substring(0, name.Length - 7);
        }
 
        Debug.Log(string.Format("Replaced {0} GameObjects", go_count));
    }

    private static void Rename()
    {
        GameObject[] go = Selection.gameObjects;
        int go_count = 0, components_count = 0, missing_count = 0;
        foreach (GameObject g in go)
        {
            go_count++;
            string name = g.name;
            g.name = name.Substring(0, name.Length - 7);
        }

        Debug.Log(string.Format("Replaced {0} GameObjects", go_count));
    }
}

Thx, but Undo (Ctrl + z) does not work