public class Tool: EditorWindow
{
    [MenuItem("Tool/Create Prefab", false, -10)]
    private static void CreatePrefab(UnityEditor.MenuCommand command)
    {

        GameObject selectedOb = (GameObject)command.context;
        Transform selectedTransform = selectedOb.transform;
        GameObject rootObject = selectedTransform.root.gameObject;

        string path = EditorUtility.SaveFilePanel("Save Prefab", "Assets/MyPrefabs", rootObject.name, "prefab");

        if (!string.IsNullOrEmpty(path))
        {
            path = FileUtil.GetProjectRelativePath(path);
            GameObject obj = selectedOb;
            PrefabUtility.SaveAsPrefabAssetAndConnect(obj, path, InteractionMode.UserAction);
        }
    }

    private static string _path_to_all_level_scenes = "";
    private static string _path_to_all_bosslevel_scenes = "";
    private static string _path_to_level_prefab_dest = "";
    private static string _path_to_bosslevel_prefab_dest = "";


    [MenuItem("Tool/Create Prefab(s)", false, -10)]

    private static void CreateAllLevelPrefabs()
    {
        string[] files = Directory.GetFiles(_path_to_all_level_scenes, "*.unity");

        foreach (string file in files)
        {
            // string sceneName = Path.GetFileNameWithoutExtension(file);
            ProcessSceneToPrefab(file, _path_to_level_prefab_dest);
        }
    }

    [MenuItem("Tool/Create Prefab(s) - Boss Level", false, -10)]

    private static void CreateAllBossLevelPrefabs()
    {
        string[] files = Directory.GetFiles(_path_to_all_bosslevel_scenes, "*.unity");

        foreach (string file in files)
        {
            // string sceneName = Path.GetFileNameWithoutExtension(file);
            ProcessSceneToPrefab(file, _path_to_bosslevel_prefab_dest);
        }
    }

    private static void ProcessSceneToPrefab(string path_to_scene, string destination)
    {
        int count = EditorSceneManager.sceneCount;

        for (int i = 0; i < count; i++)
        {
            Scene sceneI = SceneManager.GetSceneAt(i);
            Debug.LogError("Remove scene: " + sceneI.name);
            if (sceneI.buildIndex != SceneManager.GetActiveScene().buildIndex)
            {
                EditorSceneManager.UnloadSceneAsync(sceneI);
            }
        }


        Scene scene = EditorSceneManager.OpenScene(path_to_scene, OpenSceneMode.Single);
        //var allObjects = 
        //GameObject myGameObject = GameObject.Find("GameController");

        //if (myGameObject != null)
        //{
        //    string prefabPath = destination + "/" + scene.name + ".prefab";
        //    PrefabUtility.SaveAsPrefabAsset(myGameObject, prefabPath);
        //}
        GameObject root = new GameObject("PrefabRoot");

        var allGameObjectsInScene = GameObject.FindObjectsOfType<Transform>();
        foreach (var t in allGameObjectsInScene)
        {
            if (t.name == "Directional Light")
                continue;
            if (t.name == "Canvas")
                continue;
            if (t.name == "Main Camera")
                continue;
            if (t.name == "AudioManager")
                continue;
            if (t.parent == null)
            {
                t.parent = root.transform;
                continue;
            }

        }
        // Save the prefab
        string path = destination + "/" + scene.name + ".prefab";
        if (!string.IsNullOrEmpty(path))
        {
           // path = FileUtil.GetProjectRelativePath(path);
          //  PrefabUtility.SaveAsPrefabAssetAndConnect(root, path, InteractionMode.UserAction);
            PrefabUtility.SaveAsPrefabAsset(root, path);

        }
    }
}