A system and method use a substrate with a pattern of individual, indiscrete alignment marks, i.e., the marks are separate and distinct from each other, and each mark is not divided into component parts. The pattern of marks is distributed over an area of the substrate, and the method also comprises the steps of providing a beam of radiation using an illumination system and an array of individually controllable elements to impart the beam with a pattern in its cross-section, providing a projection system to project the patterned beam onto the substrate, and providing a movement system to effect relative movement between the substrate and the projection system. A detection system, able to detect the alignment marks individually, is also provided, and the method includes using the detection system to detect the marks to determine a relative position of the substrate to the projection system, using the movement system to position the substrate relative to the projection system, and using the projection system to project the patterned beam of radiation onto a target portion of the substrate. The pattern comprises one or more rows of simple alignment marks, such as spots and short linear marks.