Method and apparatus for measuring a structure on a substrate

As increasing numbers of layers, using increasing numbers of specific materials, are deposited on substrates, it becomes increasingly difficult to detect alignment marks accurately for, for example, applying a desired pattern onto a substrate using a lithographic apparatus, in part due to one or more of the materials used in one or more of the layers being wholly or partially opaque to the radiation used to detect alignment marks. In a first step, the substrate is illuminated with excitation radiation. In a second step, at least one effect associated with a reflected material effect scattered by a buried structure is measured. The effect may, for example, include a physical displacement of the surface of the substrate. In a third step, at least one characteristic of the structure based on the measured effect is derived.