Marker structure and method for controlling alignment of layers of a multi-layered substrate

The invention includes a lithographic system having a first source for generating radiation with a first wavelength and an alignment system with a second source for generating radiation with a second wavelength. The second wavelength is larger than the first wavelength. A marker structure is provided having a first layer and a second layer. The second layer is present either directly or indirectly on top of said first layer. The first layer has a first periodic structure and the second layer has a second periodic structure. At least one of the periodic structures has a plurality of features in at least one direction with a dimension smaller than 400 nm. Additionally, a combination of the first and second periodic structure forms a diffractive structure arranged to be illuminated by radiation with the second wavelength.