We demonstrate that the magnetic nano-Skyrmion lattice on the Fe monolayer on Ir(111) and the positions of the Fe atoms can be resolved simultaneously using magnetic exchange force microscopy. Thus, the relation between magnetic and atomic structure can be determined straightforwardly by evaluating the Fourier transformation of the real space image data. We further show that the magnetic contrast can be mapped on a Heisenberg-like magnetic interaction between tip and sample spins. Since our imaging technique is based on measuring forces, our observation paves the way to study Skyrmions or other complex spin textures on insulating sample systems with atomic resolution.