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The atomic force microscope (AFM) has been widely used to manipulate nanoparticles, nanowires, and nanotubes for applications such as nanostructure building, nanocharacterization, and biomanipulation. However, conventional AFM-based nanomanipulation is inefficient because of the serial scan-manipulation-scan process involved. In this paper, high-efficiency automated nanomanipulation with a parallel imaging/manipulation force microscope (PIMM) is presented. With the PIMM, image scan and nanomanipulation can be performed in parallel through the collaboration between two cantilevers: one cantilever acts as an imaging sensor and the other is used as a manipulating tool. Two automated manipulation schemes were introduced for normal- and high-speed image scanning, respectively. An automated parallel manipulation task is managed by system control software with multithread through a procedure of dynamic image processing, task planning, two-tip collaboration, and a controlled pushing manipulation with amplitude feedback from the cantilevers. The efficiency of automated parallel nanomanipulation with normal-speed image scanning was validated by building nanoparticle patterns.