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Hi tbondar,

If you are using move_base with costmap_2d, the layers of the costmap can be enabled/disabled using the dynamic reconfigure server. If you have your system running, and use:

rosrun rqt_reconfigure rqt_reconfigure

You can manually enable/disable the obstacle layer and let move_base etc path plan using other layers. If you want to make your own node to do this on your behalf take a look at running a dynamic reconfigure client.