A method for preparing a topographically structured hydrogel microarray is described comprising the steps of a) providing one or more types of biomolecule(s) on top of micropillars of an array of micropillars, preferably by means of robotical spotting, b) providing a partially crosslinked hydrogel on a substrate, preferably attached to a substantially rigid and/or planar sub- strate, c) simultaneously soft-embossing a hydrogel microwell array and transferring the biomolecule(s) from the micropillars to the microwells by pressing the micropillars of the array of step a) onto the partially crosslinked layer of hydrogel of step b) until substantial completion of crosslinking and d) demolding the array of micropillars of step a) from the hydrogel microwell array of step c). The method according to the invention has the advantages of resulting in higher biochemical patterning precision, allowing for modulation of biochemical parameters by interfacing microarray manufacture with robotic technology and rendering the microarrays obtained compatible with existing read-out systems such as microscopes. Further, the elasticity of the hydrogel can be varied by tuning its shear modulus.