Block copolymer (BCP) self-assembly in thin film is an elegant method to generate nanometric features with tunable geometrical configurations. By combining directed assembly and hybridization methods, advances in nano-manufacturing have been attested over the past decades with flagship applications in lithography and optics. Nevertheless, the range of geometrical configurations is limited by the accessible morphologies inherent to the energy minimization process involved in BCP self-assembly. Layering of nanostructured BCP thin films has been recently proposed in order to enrich the span of nanostructures derived from BCP self-assembly with the formation of non-native heterostructures such as double-layered arrays of nanowires or dots-on-line and dots-in-hole hierarchical structures. In this work, we further exploited the layer-by-layer method for the generation of nano-mesh arrays using nanostructured BCP thin films. In particular, we leveraged a subtle combination of chemical and topographical fields in order to demonstrate design rules for the controlled registration of a BCP layer on top of an underneath immobilized one by the precise tuning of the interfacial chemical field between the two BCP layers.