Controlling magnetism in low dimensional materials is essential for designing devices that have feature sizes comparable to several critical length scales that exploit functional spin textures, allowing the realization of low-power spintronic and magneto-electric hardware.[1] Unlike conventional covalently-bonded bulk materials, van der Waals (vdW)-bonded layered magnets[2-4] offer exceptional degrees of freedom for engineering spin textures. However, their structural instability has hindered microscopic studies and manipulations. Here, we demonstrate nanoscale structural control in the layered magnet CrSBr creating novel spin textures down to the atomic scale. We show that it is possible to drive a local structural phase transformation using an electron beam that locally exchanges the bondings in different directions, effectively creating regions that have vertical vdW layers embedded within the horizontally vdW bonded exfoliated flakes. We calculate that the newly formed 2D structure is ferromagnetically ordered in-plane with an energy gap in the visible spectrum, and weak antiferromagnetism between the planes. Our study lays the groundwork for designing and studying novel spin textures and related quantum magnetic phases down to single-atom sensitivity, potentially to create on-demand spin Hamiltonians probing fundamental concepts in physics,[5-9] and for realizing high-performance spintronic, magneto-electric and topological devices with nanometer feature sizes.[10,11]