Electron-beam mastering of templates for patterned media presents a challenge to the toolmaker to simultaneously meet throughput, resolution and placement requirements. Fundamental to tool development is the ability to measure the placement to true grid of shapes as small as 7 nm over the whole substrate. In this article we describe a technique, consisting of acquiring and analyzing scanning electron (SE) micrographs, for measuring the placement errors in lithography similar to that required for patterned media, albeit over a few square microns and without scale and orthogonality components. The method enabled the measurement of placement errors of dots in an array with accuracy down to about 2 nm. The technique was used to benchmark current X-Y tool performance and the smallest 3× standard deviation of placement error was found to be around 4.5 nm. A clearer understanding of the necessary tool improvements was obtained. The use of the technique as basis for measuring errors to true grid over the entire substrate is discussed.