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Correct me if I'm wrong, you want a way to prevent your robot from planning through certain areas without having to actually have anything there (what you called "logical obstacles")? If that's the case then you can just draw black lines on your map to prevent move_base from planning a path through the areas that you don't want the robot to go. You can use (the unfortunately named) GIMP image manipulator. Any areas colored black will be considered to be occupied and therefore shouldn't have any paths planned through them.

Now, if you want to constrain amcl somehow, you can use the ~laser_max_range parameter to change the maximum scan range considered.