A method for forming a functionalised guide pattern for the self-assembly of a block copolymer by graphoepitaxy, includes forming a guide pattern made of a first material having a first chemical affinity for the block copolymer, the guide pattern having a cavity with a bottom and side walls; grafting a functionalisation layer made of a second polymeric material having a second chemical affinity for the block copolymer, the functionalisation layer having a first portion grafted onto the bottom of the cavity and a second portion grafted onto the side walls of the cavity; selectively etching the second portion of the functionalisation layer relative to the first portion of the functionalisation layer, the etching including a step of exposure to an ion beam following a direction that intersects the second portion of the functionalisation layer, such that the ion beam does not reach the first portion of the functionalisation layer.