Due to the increasing demand of high accuracy in printed electronics industry at a micrometer-level, it is necessary to have a precise control scheme for web velocity and tension in the presence of disturbances. In this paper, a generalized mathematical model of non-linear control system is proposed and a systematic procedure is presented to design a backstepping controller taking the modified backstepping approach. With application of the proposed theory, a precise control algorithm is developed for a nonlinear two-span roll-to-roll web control system based on the backstepping method. The design parameters are chosen optimally by using the modified genetic algorithm. The reliability of the proposed algorithm is validated through simulations in Matlab/Simulink and real experiments.