Harmonic drives are popular in precision positioning applications such as military radars, satellite cameras, and wafer alignment machines because of their unique property of near-zero backlash. However, precision positioning performance is degraded by non-linear effects of inherent kinematic error and flexibility. This paper presents new non-linear controller development along with experimental veri. cation to compensate for kinematic error in the presence of flexibility in high-speed regulation and trajectory tracking applications. Several issues in implementation of complex theoretical controllers in experiments have been discussed. The development uses our previous algorithms to compensate only for the kinematic error ignoring flexibility effects ( U. S. Patent 6,459,940). The proposed control development is based on recent results on the integral manifold approach and guarantees asymptotic stability. We present simulation and experimental results to further demonstrate the effectiveness of our approach for practical application. Our results thus establish a solid basis for high-speed, high-precision control design for harmonic drive systems.