Auto focus using multiple location illumination

An auto-focus system, comprising:

• an illumination path that is configured to illuminate a front surface of a sample during scanning, the illumination path including illumination beams that form multiple spot arrays on the sample, the multiple spot arrays comprising an upstream set of spot arrays formed on the front surface of the sample and on a first side of an imaging area, and a downstream set of spot arrays formed on the front surface of the sample and on an opposite side of the imaging area from the upstream set of spot arrays;
• a sensor;
• a controller;
• and
• a collection path that comprises an entrance pupil and is configured to collect collected beams that are emitted from the sample and correspond to the multiple spot arrays, the collection path configured to image the entrance pupil to provide optically processed beams;
• wherein the sensor is configured to generate detection signals that represent the optically processed beams;
• and wherein the controller is configured to determine a focus state of an evaluation beam that impinges on the imaging area based on the detection signals,
• wherein the upstream set of spot arrays includes at least a first upstream spot array and a second upstream spot array, and the first upstream spot array is staggered from the second upstream spot array along both a first axis and a second axis, and the downstream set of spot arrays includes at least a first downstream spot array and a second downstream spot array, and the first downstream spot array is staggered from the second downstream spot array along both the first axis and the second axis.