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This paper presents a nanomanipulation system for operation inside scanning electron microscopes (SEM). The system is compact, making it capable of being mounted onto and demounted from an SEM through the specimen-exchange chamber (load-lock) without breaking the high vacuum of the SEM. This advance avoids frequent opening of the high-vacuum chamber, thus, incurs less contamination to the SEM, avoids lengthy pumping, and significantly eases the exchange of end effectors (e.g., nanoprobes and nanogrippers). The system consists of two independent 3-DOF Cartesian nanomanipulators driven by piezomotors and piezoactuators. High-resolution optical encoders are integrated into the nanomanipulators to provide position feedback for closed-loop control. The system is characterized, yielding the encoders' resolution of 2 nm and the piezoactuators' resolution of 0.7 nm. A look-then-move control system and a contact-detection algorithm are implemented for horizontal and vertical nanopositioning.