A method of measuring properties of a sample using an electron beam. Coordinates of a measurement site on the sample, and a diameter of the electron beam are defined. Multiple measurement locations are determined within the measurement site, using the coordinates of the measurement site and the diameter of the electron beam. The measurement locations are selected such that the electron beam when directed at the multiple measurement locations (either through beam deflection or sample movement) substantially covers the measurement site. The electron beam is directed to the measurement locations and properties of the sample are measured at each of the measurement locations.