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Remove the passthrough filter with a z-range limit.

There is a configurable z-range limit which you can configure instead directly in octomap_server. You should include enough of the z range so that the ground plane can be used for clearing obstacles. When you cut it away, you can no longer clear obstacles in between. Instead, just enable the ground plane filter in octomap_server, it will clear properly.

Remove the passthrough filter with a z-range limit.

There is a configurable z-range limit which you can configure instead directly in octomap_server. You should include enough of the z range so that the ground plane can be used for clearing obstacles. When you cut it away, you can no longer clear obstacles in between. Instead, just enable the ground plane filter in octomap_server, it will clear properly.

Edit regarding voxel grid filter: It's usually a good idea to run that in order to speed up the integration in OctoMap. However, you must choose a resolution at most as small as your octomap resolution.