This paper introduces a low-cost, automated wafer alignment system capable of submicron wafer positioning repeatability. Accurate wafer alignment is critical in a number of nanomanufacturing and nanometrology applications where it is necessary to be able to overlay patterns between fabrication steps or measure the same spot on a wafer over and over again throughout the manufacturing process. The system presented in this paper was designed to support high-throughput nanoscale metrology where the goal is to be able to rapidly and consistently measure the same features on all the wafers in a wafer carrier without the need for slow and expensive vision-based alignment systems to find and measure the desired features. The wafer alignment system demonstrated in this paper consists of a three-pin passive wafer alignment stage, a voice coil actuated nesting force applicator, a three degrees-of-freedom (DOFs) wafer handling robot, and a wafer cassette. In this system, the wafer handling robot takes a wafer from the wafer cassette and loads it on to the wafer alignment stage. The voice coil actuator is then used to load the wafer against the three pins in the wafer alignment system and align the wafer to an atomic force microscope (AFM)-based metrology system. This simple system is able to achieve a throughput of 60 wafers/h with a positional alignment repeatability of 283 nm in the x-direction, 530 nm in the y-direction, and 398 nm in the z-direction for a total capital cost of less than $1800.