Automated scanning transmission electron microscopy (STEM) metrology provides critical dimension (CD) measurements an order of magnitude more precise than comparable scanning electron microscopy (SEM) measurements. New developments in automation now also provide throughput and response time sufficient to support high volume microelectronic manufacturing processes. The newly developed methodology includes automated, focused ion beam (FIB) based sample preparation; innovative, ex-situ sample extraction; and automated metrology. Although originally developed to control the production of thin film magnetic heads for data storage, the technique is fully applicable to any wafer-based manufacturing process.