A medical robotic system includes an entry guide with articulated instruments extending out of its distal end. A controller is configured to command manipulation an articulated instrument in response to operator manipulation of an associated input device while generating a force command to the input device that nudges the operator to command the instrument to a preferred pose. When a transition is to occur between first and second preferred poses, one is phased in while the other is phased out. Virtual barriers may be imposed to prevent the articulated instrument from being commanded to an undesirable pose.
