Can I ignore trees when baking NavMesh on Terrain?

I had the same problem, my only solution was delete all the trees with the big Brush, Bake the NavMesh, and then undo with Ctrl + z.

In that way you can keep your artist modifications and have the proper nav mesh.

It's far from be elegant, but Im running out of ideas.

This is a glaring oversight and a big pain in my butt. Why does the navmesh generator completely ignore the "create tree collider" option? Now my AI carefully avoids stepping on any tiny plants or grass even though none of them have a collider attached. It's ridiculous.

Is this problem submitted in the bugs forum? Having to erase all foliage, then generating navmesh, then ctrl-z ing everything back is cumbersome. And what if you need to have walkable shrubs but you need trees to block paths? It can't be done unless you add shrubs at the very last step of level creation. This is a SERIOUSLY ANNOYING limitation.

Fixed it by creating a small script which first erases all trees and then restores them:

 using System.Collections.Generic;
 using System.Linq;
 using UnityEditor;
 using UnityEditor.AI;
 using UnityEngine;
 using UnityEngine.SceneManagement;
 
 public class TerrainNavMeshBaker 
 {
     private static Dictionary<Terrain, TreeInstance[]> _terrainTrees = new Dictionary<Terrain, TreeInstance[]>();
 
     [MenuItem("Tools/Bake NavMesh")]
     public static void BakeNavMesh()
     {
         try
         {
             RemoveTrees();
             NavMeshBuilder.BuildNavMesh();
         }
         finally
         {
             RestoreTrees();
         }
     }
 
     private static void RestoreTrees()
     {
         foreach (var terrain in _terrainTrees)
         {
             terrain.Key.terrainData.treeInstances = terrain.Value;
         }
     }
 
     private static void RemoveTrees()
     {
         var terrains = new List<Terrain>();
 
         for (int i = 0; i < SceneManager.sceneCount; i++)
         {
             var scene = SceneManager.GetSceneAt(i);
 
             if (!scene.isLoaded)
                 continue;
 
             terrains.AddRange(scene.GetRootGameObjects().SelectMany(x => x.GetComponentsInChildren<Terrain>()));
         }
 
         _terrainTrees.Clear();
         foreach (var terrain in terrains)
         {
             _terrainTrees[terrain] = terrain.terrainData.treeInstances;
             terrain.terrainData.treeInstances = new TreeInstance[0];
         }
     }
 }

pipiroo6's workaround has inspired me, and i have one that some might prefer: make a prefab of an empty game object, and when you need to bake, hit "edit tree" and choose this prefab for all trees you want to ignore. Still not perfect, but less cumbersome for me at least.,pipiroo6's workaround has inspired me, and i have what might be a better one for some people: make a prefab of an empty game object, and when you need to bake, hit Edit Tree and replace the tree(s) in question with this prefab. then you can put the originals back when you're done baking. still not perfect, but slightly less cumbersome in my opinion.

I just found a similar answer, and it is based off of the ctrl + Z method. I had already finished my terrain, with large amounts of grass a trees, so naturally didn't want to erase everything. After reading the ctrl + Z idea, I realized that you could delete the trees (or grass) from the terrain brush tool, Re-Bake the navmesh, then press crtl + Z to replace the vegetation. It should not remove any of the vegetation after you press ctrl + Z, but i do advise saving the scene first in case something doesn't go right. I found this to be an faster solution.

I'm using Unity 2018.2