How to save a 2D-grid of instantiated GameObjects in C#?

With "save" mean a savefile for players to load and overwrite. I made a Map with perlinNoise. That part works fine, it creates a 200x200 gridfield of diffrent terrainfields.

The player should be able to change the map in diffrent ways, like buildings, explosions and stuff like that. So I can not just generate the Map again.

For other values to save I use a Binary Formatter. But I have no idea how to save every gridcell with its information and postion.

Here is my script for generating the map:

 private Dictionary<int, GameObject> tileset;
 private Dictionary<int, GameObject> tileGroups;
 public GameObject[] mapTiles = new GameObject[0];

 public int seed;

 public int mapWidth;
 public int mapHeight;
 private Vector2 GSL; //GenerationStartingLocation

 private List<List<int>> noiseGrid = new List<List<int>>();
 private List<List<GameObject>> tileGrid = new List<List<GameObject>>();

 //Detail (recommended between 4 and 20)
 public float magnification;

 public int xOffset;
 public int yOffset;

 private void Start()
 {
     GSL.x = -mapWidth / 2;
     GSL.y = -mapWidth / 2;
     CreateTileset();
     CreateTileGroups();
     GenerateMap();
 }
 private void CreateTileset()
 {
     tileset = new Dictionary<int, GameObject>();
     tileset.Add(0, mapTiles[0]);
     tileset.Add(1, mapTiles[1]);
     tileset.Add(2, mapTiles[2]);
     tileset.Add(3, mapTiles[3]);
     tileset.Add(4, mapTiles[4]);
 }
 private void CreateTileGroups()
 {
     tileGroups = new Dictionary<int, GameObject>();
     foreach(KeyValuePair<int, GameObject> prefab_pair in tileset)
     {
         GameObject tileGroup = new GameObject(prefab_pair.Value.name);
         tileGroup.transform.parent = this.transform;
         tileGroup.transform.localPosition = new Vector3(0, 0, 0);
         tileGroups.Add(prefab_pair.Key, tileGroup);
     }
 }
 private void GenerateMap()
 {
     for (int x = 0; x < mapWidth; x++)
     {
         noiseGrid.Add(new List<int>());
         tileGrid.Add(new List<GameObject>());
         for (int y = 0; y < mapHeight; y++)
         {
             int tileID = GetIdUsingPerlin(x, y);
             noiseGrid[x].Add(tileID);
             CreateTile(tileID, x, y);
         }
     }
 }   
 private int GetIdUsingPerlin(int x, int y)
 {
     float rawPerlin = Mathf.PerlinNoise((x - xOffset + seed) / magnification, (y - yOffset + seed) /magnification);
     float clampPerlin = Mathf.Clamp(rawPerlin, 0.0f, 1.0f);
     float scaledPerlin = clampPerlin * tileset.Count;
     if(scaledPerlin >= mapTiles.Length)
     {
         scaledPerlin = mapTiles.Length - 1;
     }
     return Mathf.FloorToInt(scaledPerlin);
 }
 private void CreateTile(int tileID, int x, int y)
 {
     GameObject tilePrefab = tileset[tileID];
     GameObject tileGroup = tileGroups[tileID];
     GameObject tile = Instantiate(tilePrefab, tileGroup.transform);

     tile.name = string.Format("tileX{0}_Y{1}", x, y);
     tile.transform.localPosition = new Vector3(x + GSL.x, y + GSL.y, 0);

     tileGrid[x].Add(tile);
 }

As you can see, the script also generates Folders containing the MapTiles. So maybe there is a way to save these folders?