We report on both the global and micromagnetic properties of interlayer exchange coupled spin systems. Irradiation with Ne ions is employed to achieve a phase transition from antiferromagnetic to ferromagnetic coupling. For extended trilayer films a full quantitative analysis of the bilinear and biquadratic coupling constants is performed. With increasing ion fluence we observe a steady increase of the bilinear coupling constant at an almost negligible decrease in saturation magnetization. The mixing of atoms at the layer interfaces is identified as the origin for this. The effects of ion modification on the magnetic microstructure are studied for the model system of layered vortex pairs. X-ray microscopy is used to directly image the individual magnetization circulations in trilayer disks. The circulation configuration is found to be determined by the film coupling for both coupling orientations with a homogenous coupling angle throughout the structure. For the vortex cores, however, micromagnetic simulations indicate that due to the significant local demagnetization fields, parallel states are always energetically preferred. Nevertheless antiparallel configurations are metastable, having their signature in reduced core diameters. Our study provides new results on spin structures in interlayer exchange coupled trilayers and it demonstrates a promising way to control the local interlayer coupling post-deposition.