Replaces trees on a terrain with prefab.

TreeReplacerS.cs

using UnityEngine;
using System.Collections;
using System.Collections.Generic;
using UnityEditor;

// Replaces Unity terrain trees with prefab GameObject.
// http://answers.unity3d.com/questions/723266/converting-all-terrain-trees-to-gameobjects.html
[ExecuteInEditMode]
public class TreeReplacerS : EditorWindow {

	[Header("Settings")]
	public GameObject _tree;

	[Header("References")]
	public Terrain _terrain;


	[MenuItem("Tools/TreeReplacer")]
	static void Init()
	{
		TreeReplacerS window = (TreeReplacerS)GetWindow(typeof(TreeReplacerS));
	}

	void OnGUI()
	{
		_terrain = (Terrain)EditorGUILayout.ObjectField(_terrain, typeof(Terrain), true);
		_tree = (GameObject)EditorGUILayout.ObjectField(_tree, typeof(GameObject), true);

		GUILayout.Label("Create");

		GUILayout.BeginHorizontal();

		if (GUILayout.Button("Convert (Keep Previous)", GUILayout.Height(40f)))
		{
			Convert();
		}

		if (GUILayout.Button("Convert (Clear Previous)", GUILayout.Height(40f)))
		{
			Clear();
			Convert();
		}

		GUILayout.EndHorizontal();


		GUILayout.Label("Destroy");

		GUILayout.BeginHorizontal();

		Color oldColor = GUI.backgroundColor;
		GUI.backgroundColor = Color.red;

		if (GUILayout.Button("Clear generated trees", GUILayout.Height(40f)))
		{
			Clear();
		}

		if (GUILayout.Button("ClearTerrainTreeInstances", GUILayout.Height(40f)))
		{
			ClearTerrainTreeInstances();
		}
		GUI.backgroundColor = oldColor;

		GUILayout.EndHorizontal();
	}

	public void Convert()
	{
		TerrainData data = _terrain.terrainData;
		float width = data.size.x;
		float height = data.size.z;
		float y = data.size.y;

		// Create parent
		GameObject parent = GameObject.Find("TREES_GENERATED");

		if (parent == null)
		{
			parent = new GameObject("TREES_GENERATED");
		}

		// Create trees
		for (int i = 0; i < data.treeInstances.Length; i++)
		{
			TreeInstance tree = data.treeInstances[i];

			//Vector3 position = new Vector3(tree.position.x * width, tree.position.y * y, tree.position.z * height);
			Vector3 position = new Vector3(tree.position.x * data.detailWidth - (data.size.x / 2), tree.position.y * y - (data.size.y / 2), tree.position.z * data.detailHeight - (data.size.z / 2));

			// Instantiate as Prefab if is one, if not, instantiate as normal
			GameObject go = PrefabUtility.InstantiatePrefab(_tree) as GameObject;

			if (go != null)
			{
				go.name += " (" + i.ToString() + ")";
				go.transform.position = position;
				go.transform.parent = parent.transform;
			}
			else
			{
				Instantiate(_tree, position, Quaternion.identity, parent.transform);
			}
		}
	}

	public void Clear()
	{
		DestroyImmediate(GameObject.Find("TREES_GENERATED"));
	}

	public void ClearTerrainTreeInstances()
	{
		_terrain.terrainData.treeInstances = new List<TreeInstance>().ToArray();
	}

}

using UnityEngine;
using System.Collections;
using System.Collections.Generic;
using UnityEditor;

// Replaces Unity terrain trees with prefab GameObject.
// http://answers.unity3d.com/questions/723266/converting-all-terrain-trees-to-gameobjects.html
[ExecuteInEditMode]
public class TreeReplacerS : EditorWindow
{

[Header("Settings")]

[Header("References")]
public Terrain _terrain;

string savedTreesName = "SAVED_TREES_TERRAIN_";
string convertedParentName = "CONVERTED_TREES_TERRAIN_";


[MenuItem("Tools/TreeReplacer")]
static void Init()
{
	TreeReplacerS window = (TreeReplacerS)GetWindow(typeof(TreeReplacerS));
}

void OnGUI()
{
	// _terrain = (Terrain)EditorGUILayout.ObjectField(_terrain, typeof(Terrain), true);

	GUILayout.Label("Create");

	GUILayout.BeginHorizontal();

	if (GUILayout.Button("Convert (Clear Previous)", GUILayout.Height(40f)))
	{
		ClearAll();
		ConvertAll();
	}

	GUI.backgroundColor = Color.red;
	if (GUILayout.Button("Clear AllTerrainTreeInstances", GUILayout.Height(40f)))
	{
		ClearAllTerrainTreeInstances();
	}
	GUILayout.EndHorizontal();

	GUILayout.BeginHorizontal();

	GUI.backgroundColor = Color.green;

	if (GUILayout.Button("Save (Current Trees)", GUILayout.Height(40f)))
	{
		Savetrees();
	}
	GUILayout.EndHorizontal();

	GUILayout.BeginHorizontal();

	GUI.backgroundColor = Color.red;

	if (GUILayout.Button("Delete (Converted Trees)", GUILayout.Height(40f)))
	{
		DeleteConvertedTrees();
	}

	if (GUILayout.Button("Delete (Saved Trees)", GUILayout.Height(40f)))
	{
		DeleteSavedTrees();
	}
	GUILayout.EndHorizontal();

}

public void Convert(Terrain terrain, string parentName)
{
	TerrainData data = terrain.terrainData;
	float width = data.size.x;
	float height = data.size.z;
	float y = data.size.y;

	// Create parent
	GameObject parent = GameObject.Find(parentName);

	if (parent == null)
	{
		parent = new GameObject(parentName);
	}

	parent.transform.parent = terrain.transform;
	parent.transform.localPosition = Vector3.zero;

	// Create trees
	for (int i = 0; i < data.treeInstances.Length; i++)
	{
		TreeInstance tree = data.treeInstances[i];
		GameObject _tree = data.treePrototypes[tree.prototypeIndex].prefab;

		//Vector3 position = new Vector3(tree.position.x * width, tree.position.y * y, tree.position.z * height);
		Vector3 position = Vector3.Scale(tree.position, data.size) + terrain.transform.position;

		// Instantiate as Prefab if is one, if not, instantiate as normal
		GameObject go = PrefabUtility.InstantiatePrefab(_tree) as GameObject;

		if (go != null)
		{
			go.name += " (" + i.ToString() + ")";
			go.transform.position = position;
			go.transform.parent = parent.transform;
		}
		else
		{
			Instantiate(_tree, position, Quaternion.identity, parent.transform);
		}

		Transform treeTransform = go.transform;
		// set correct Scale of tree instance
		treeTransform.localScale = new Vector3(tree.widthScale, tree.heightScale, tree.widthScale);
		// set random rotation
		RotateTrees(treeTransform.transform);
		// set correct slope of tree
		RotateToMatchTerrainSlope(treeTransform, terrain);

	}

}
public void ConvertAll()
{
	Terrain[] terrains = GetAllTerrains();

	for (int i = 0; i < terrains.Length; i++)
    {
		Convert(terrains[i], (convertedParentName + i));
    }
}

Terrain[] GetAllTerrains()
{
	return GameObject.FindObjectsOfType<Terrain>();
}

public void ClearAll()
{
	List<GameObject> allGeneratedTrees = new List<GameObject>();

   for (int i = GetAllTerrains().Length - 1; i >= 0; i--)
    {
		allGeneratedTrees.Add(GameObject.Find("TREES_GENERATED"+i));
    }

    for (int i = allGeneratedTrees.Count - 1; i >= 0; i--)
    {
		GameObject parentObj = allGeneratedTrees[i];
		allGeneratedTrees.Remove(parentObj);
		DestroyImmediate(parentObj);

	}
}

public void ClearAllTerrainTreeInstances()
{
	Terrain[] terrains = GetAllTerrains();

	for (int i = 0; i < terrains.Length; i++)
    {
		terrains[i].terrainData.treeInstances = new List<TreeInstance>().ToArray();
    }
}
public void Savetrees()
{
	Terrain[] terrains = GetAllTerrains();


    for (int i = 0; i < terrains.Length; i++)
    {
		GameObject parent = GameObject.Find(convertedParentName+i);

		if (parent != null) 
		parent.name = savedTreesName + i;
		else
        {
			Debug.Log("Cant find Converted Trees");
        }
	}
}

public void DeleteConvertedTrees()
{
	Terrain[] terrains = GetAllTerrains();

	for (int i = 0; i < terrains.Length; i++)
	{
		GameObject parent = GameObject.Find(convertedParentName + i);

		DestroyImmediate(parent);
	}
}
public void DeleteSavedTrees()
{
	Terrain[] terrains = GetAllTerrains();


	for (int i = 0; i < terrains.Length; i++)
	{
		GameObject parent = GameObject.Find(savedTreesName+i);

		DestroyImmediate(parent);
	}
}
void RotateTrees(Transform target)
{
	float randomRotation = Random.Range(0, 360);

	target.transform.RotateAround(target.transform.position, target.transform.up, randomRotation);
}
void RotateToMatchTerrainSlope(Transform target, Terrain terrain)
{
	RaycastHit hit;
	if (Physics.Raycast(target.position, Vector3.down, out hit))
	{
		target.rotation = Quaternion.FromToRotation(terrain.transform.up, hit.normal) * target.rotation;
	}
}

}