In this work we investigate the use of state-of-the-art tools for the regulation of complex, non-linear systems to improve the methodologies currently applied to trim comprehensive virtual prototypes of rotors and rotorcrafts. Among the several methods that have been proposed in the literature, the auto-pilot approach has the potential to solve trim problems efficiently even for the large and complex vehicle models of modern comprehensive finite element-based analysis codes. In this approach, the trim condition is obtained by adjusting the controls so as to virtually ``fly' the system to the final steady (periodic) flight condition. Published proportional auto-pilots show to work well in many practical instances. However, they cannot guarantee good performance and stability in all flight conditions of interest. Limit-cycle oscillations in control time histories are often observed in practice because of the non-linear nature of the problem and the difficulties in enforcing the constant-in-time condition for the controls. To address all the above areas of concern, in this research we propose a new auto-pilot, based on non-linear model-predictive control (NMPC). The formulation uses a non-linear reference model of the system augmented with an adaptive neural element, which identifies and corrects the mismatch between reduced model and controlled system. The methodology is tested on the wind-tunnel trim of a rotor multibody model and compared to an existing implementation of a classic auto-pilot. The proposed controller shows good performance without the need of a potentially very expensive tuning phase, which is required in classical auto-pilots. Moreover, model-predictive control provides a framework for guaranteeing stability of the non-linear closed-loop system, so it seems to be a viable approach for trimming complete rotorcraft comprehensive models in free-flight.