Nanoassembly using atomic force microscopy (AFM) is a promising technique for nanomanufacturing. Most AFM-based nanoassembly schemes are implemented either manually using haptic devices or in an interactive way between the users and the atomic force microscope images. These schemes are time consuming and inefficient. Therefore, the computer-aided design (CAD)-guided automated nanoassembly using AFM is desirable for nanomanufacturing. In this paper, a general framework for CAD-guided automated nanoassembly using AFM is developed. Based on the CAD model of a nanostructure, the manipulation paths for both nanoparticles and nanorods are generated automatically. A local scanning method is developed to compensate for the random drift that may cause the failure of the nanoassembly. The experimental results demonstrate that the developed general framework can be employed to manufacture nanostructures efficiently. The research work opens a door to the CAD-guided automated nanomanufacturing using AFM. Note to Practitioners-Atomic force microscope (AFM)-based nanoassembly will lead to potential breakthroughs in manufacturing new revolutionary industrial products because many potential nanostructures and nanodevices are asymmetric, which cannot be manufactured using self-assembly only. In order to increase the efficiency and accuracy of AFM-based nanoassembly, automated computer-aided-design (CAD)-guided nanoassembly is desirable to manufacture nanostructures and nanodevices. Based on the CAD model, the environment model and the model of the nanoobjects, collision-free paths are generated to control the AFM tip to manipulate nanoobjects. A local scanning method is developed to obtain the actual position of each nanoobject to compensate for the random drift. Since the building materials of nanostructures and nanodevices may include nanoparticles, nanorods, nanowires, nanotubes, etc., automated path planning algorithms are developed for both nanoparticles and nanorods. The experimental results show that the developed general framework can be used to manufacture nanostructures more efficiently.