We report on large-scale fabrication of wrinkled polyelectrolyte multilayers (PEMs) with well-defined surface relief structures by embossing. The embossed assembly films show hierarchical topography consisting of patterns on the micrometer scale defined by the stamp used for embossing that are decorated by stable and highly regular patterns on the submicrometer scale. The periodicities of the concentric wrinkles can be controlled well down to 250 nm. We propose that a new mechanism of combining inelastic deformation of the support and selective wetting by the PEM film to be responsible for the above wrinkling with high stability in the wet state and enhanced aspect ratio.