System and method for hierarchy reconstruction from a flattened layout are described. In one embodiment, a method for producing a reconstructed layout for an integrated circuit design from an original layout and a revised layout includes, for each pattern of the original layout, determining a pattern of the revised layout that corresponds to the pattern of the original layout; and assigning the corresponding pattern of the revised layout to a temporary instance, the temporary instance corresponding to an instance of the pattern of the original layout and citing to a temporary cell. The method further includes creating a temporary reconstructed layout from the temporary instances; and producing the reconstructed layout from the temporary reconstructed layout, wherein a hierarchy of the reconstructed layout is similar to a hierarchy of the original layout.