For navigating in a 3D, you may want an efficiency structure for the point cloud like an octomap. You can look at the previous post "
octomap with rtabmap" to know how to generate an octomap with
octomap_server. For 3D navigation, I am not aware if there are packages using the octomap for trajectory planning, but it may have some. The
3D navigation stack looks old, but maybe it could give some ideas.
But if you are using a turtlebot, you could just plan with 2D occupancy maps?