One of the major challenges in nanoscale manufacturing is defect control because it is difficult to measure nanoscale features in-line with the manufacturing process. Optical inspection typically is not an option at the nanoscale level due to the diffraction limit of light, and without inspection high scrap rates can occur. Therefore, this paper presents an atomic force microscopy (AFM)-based inspection system that can be rapidly implemented in-line with other nanomanufacturing processes. Atomic force microscopy is capable of producing very high resolution (subnanometer-scale) surface topology measurements and is widely utilized in scientific and industrial applications, but has not been implemented in-line with manufacturing systems, primarily because of the large setup time typically required to take an AFM measurement. This paper introduces the design of a mechanical wafer-alignment device to enable in-line AFM metrology in nanoscale manufacturing by dramatically reducing AFM metrology setup time. The device consists of three pins that exactly constrain the wafer and a nesting force applied by a flexure to keep the wafer in contact with the pins. Kinematic couplings precisely mate the device below a flexure stage containing an array of AFM microchips which are used to make nanoscale measurements on the surface of the semiconductor wafer. This passive alignment system reduces the wafer setup time to less than 1 min and produces a lateral positioning accuracy that is on the order of ∼1 μm.