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The way I've typically done this in the past is to take the raw map, modify it in an image editor (without changing the size/etc). Then publish both maps (they are already aligned in space -- there is no transforms needed). Take a look at fetch_navigation and fetch_maps -- it does just this (the keepout map has been edited to draw boxes over things that would kill the robot, like desks): https://github.com/fetchrobotics/fetch_ros/tree/indigo-devel/fetch_navigation