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An automated manipulation procedure for spherical nanoparticles with an atomic force microscope (AFM) in 2-D is demonstrated. Robust particle-center and contact-loss detection algorithms are developed using force feedback to improve speed and reliability issues of AFM-based nanomanipulation. Unlike blind manipulation techniques, contact-loss detection enables better control over the success of manipulation. For pattern formation and assembly operations, a fully automated multiple-particle-manipulation method is developed, based on a commanding task planner. The task planner minimizes the obstacles to manipulation trajectories for better efficiency. Forces during AFM tip-particle-substrate contact are analyzed theoretically to determine the mode of manipulation as well as the effect of cantilever normal stiffness. The developed system is used to form patterns and assemblies of 100-nm-diameter gold nanoparticles on a flat substrate.