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();
	}

}

I used your script but changed it to convert all the terrains not just the selected terrain. and the prefab is selected from the terrain tree instance prefabs. Please give me your view on this. Thank you for the script.

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;
	}
}

}