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();
	}

}