Virtual instrumentation platforms are available today to design and implement refined algorithms for precision control of fin stabilizers. While on the one hand this non-traditional strategy obviates the need for cumbersome hardware involved in controllers and instrumentation panels, it also facilitates compact computation of the feedback control data and precise control signal on the actuators. This paper reports the implementation of a virtual instrumentation algorithm for fin control. It combines the analysis of fin lift dynamic characteristics taking into account the hull in its proximity using computational fluid dynamics (CFD). The frequency dependent hydrodynamic coefficients of the ship hull and stabilizer fin are represented in a polynomial function form. A harmonic distortion analyzer function is used to detect fundamental frequency in the error signal (roll), and using this in a feedback control loop, the control signal for the actuator is generated. The algorithm is generalized for coupled sway, roll and yaw conditions, and can be employed for single or multiple input systems. It is demonstrated in a laboratory model for induced roll disturbances. The robustness and stability of the system is brought out through numerical and experimental simulations for regular and random excitation conditions. By combining numerical hydrodynamics with virtual instrumentation, a modern control strategy is presented. © 2007 American Bureau of Shipping.