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Nanopositioning control as the key technology has been applied in many fields such as near-field optics, biomedical engineering, and nanomanipulation, where it is required to possess high positioning accuracy, reliability, and speed. In this paper, a switched PID controller-based fast setpoint control method is proposed for nanopositioning systems. In order to improve the setpoint speed of the nanopositioning system without a large overshoot, a switched controller consisting of the approach mode and smooth mode is synthesized. The overshoot constraint of the resulting switched closed-loop system is investigated within a set of bilinear matrix inequalities, based on which the search of the controller parameters can be further processed by solving the properly formulated synthesis algorithm. The proposed control method is evaluated in a nanopositioning experimental system driven by a PZT actuator, and the experimental results demonstrate the effectiveness of the switched PID controller for the fast setpoint approaching operation.