Conventional in situ hydrogel micropatterning techniques work successfully for relatively stiff hydrogels, but they often result in locally damaged surfaces upon demolding in the case of soft and fragile polymer networks formed at low precursor concentration. To overcome this limitation, we have developed a versatile method, termed soft embossing, for the topographical micropatterning of fragile chemically cross-linked polymer hydrogels. Soft embossing is based on the imprinting of a microstructured template into a gel surface that is only partially cross-linked. Free functional groups continue to be consumed and upon complete cross-linking irreversibly confine the microstructure on the gel surface. Here we identify and optimize the parameters that control the soft embossing process and show that this method allows the fabrication of desired topographies with good fidelity. Finally, one of the produced gel micropatterns, an array of microwells, was successfully utilized for culturing and analyzing live single hematopoietic stem cells. Confining the stem cells to their microwells allowed for efficient quantification of their growth potential during in vitro culturing.