Nanomanufacturing using Atomic Force Microcopy has been widely investigated. Most of nanomanipulation schemes go through the scan-design-manipulation-scan cycle manually which is time consuming and inefficient. Automated AFM tip path planning is desirable for nanomanufacturing, but does not receive much attention. In this paper, a CAD guided automated nanomanufacturing system is presented. 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 nano-assembly. The experimental results demonstrate that the developed algorithm can be employed to manufacture nanostructures efficiently. The research work opens a door to the CAD guided automated nanomanufacturing.