A method for recovering alignment marks in a mark layer of a substrate, the method including providing a substrate with a mark layer covered by a resist layer; forming alignment marks in the mark layer, wherein an alignment mark is formed by: exposing the resist layer to a patterned radiation beam thereby forming an alignment pattern in the resist; forming one or more recovery marks in the mark layer, wherein a recovery mark is formed by exposing the resist layer to at least a portion of the patterned radiation beam thereby forming an alignment pattern in a mark area of the resist and subsequently exposing the mark area of the resist, each time with a shifted patterned radiation beam until a substantial part of the mark area has been exposed.