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Hello Ivan,
What robot are you using this for? Do you have a collision checker? It seems to me what you can do is just use OMPL directly. Define a SE3StateSpace (which represents a position in space + orientation) or RealVectorStateSpace(3) (to represent just a 3D point), set the bounds for the space and plan there directly. You do need to specify your collision checker directly however. Check http://ompl.info for tutorials on how to do this, or post questions here again.
Ioan