In this article, two practical issues occurring in the design and control of scan trajectories are studied: One, the reduction of the output oscillations during the scanning, and two, the effect of the modeling errors on the output precision during the scanning. Output oscillations need to be minimized in scanning operations of systems such as the piezo actuator and the flexible structure, while modeling errors widely exists in practical applications. The proposed approach extends the recently-developed optimal scan trajectory design and control method, by introducing the design of a prefilter into the framework to reduce the output oscillations. Furthermore, a novel inversion-based iterative control algorithm is proposed and integrated with the optimal scan method to compensate for the modeling error effect on the scanning. The convergence of the iterative control law is discussed, and the convergence range is quantified. The proposed approach is illustrated by implementing it on the high-speed adhesion force measurement using AFM. Simulation and experimental results are presented and discussed to demonstrate the efficacy of the proposed approach.