An automated nanomanipulation system is provided for manufacturing a nanoscale structure. The system includes: a design model for the nanoscale structure; image data of a sample surface upon which the nanoscale structure is to be manufactured; a movable member configured to perform a nanomanipulation operation on the sample surface; and a path planning subsystem adapted to receive the design model and the image data. The path planning subsystem generates path data indicative of a path for traversing the movable member along the sample surface such that the movable member manipulates one or more randomly distributed nanoobjects in accordance with the design model.