Method and workstation automatically designing an arch-wire including compensations for auxiliary appliances or biological constraints exerting unknown forces to achieve a pre-planned treatment goal are disclosed. The adjusted customized arch-wire is designed after an initial customized arch-wire has been used to treat a patient and is at or near equilibrium. The initial custom arch-wire is first designed by producing a 3D computer-based, geometrical model of a patient's dentition, locating brackets on the digital tooth model, moving the digital tooth models to planned final positions and orientations, and then calculating a wire which fits in the slots of the brackets while the teeth are in their planned final positions and exerts no forces on the brackets. After a period of time the teeth will move under the force of the wire and will eventually move into positions such that the forces from all appliances and biological systems are in equilibrium. If the teeth are not in the final planned positions at that point in time, the adjusted custom arch-wire is designed and applied.