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Depth resolved study of structural and magnetic profiles of antiferromagnetic/ferromagnetic (AFM/FM) system upon annealing was performed in this work. We studied systems comprising of AFM IrMn and FM (Co, Fe, Co$_{70}$Fe$_{30}$) structures using polarized neutron and soft X-ray scattering, secondary neutral spectrometry, and magnetometry. Structural depth profiles obtained from neutron reflectometry indicate non-homogeneity of the AFM layer even before annealing, which is associated with the migration of manganese to the surface of the sample. Annealing of samples with CoFe and Co layers leads to a slight increase ($\sim$ 5 %) in the migration of manganese, which, however, does not lead to significant degradation of the exchange coupling at the AFM/FM interface. A significantly different picture was observed in the Fe/IrMn systems where a strong migration of iron into the AFM layer was observed upon annealing of the sample, leading to erosion of the magnetic profile, the formation of a non-magnetic alloy and degradation of the pinning strength. This study can be useful in the design of AF/FM systems in different spintronics devices, including HDD read heads, where thermal annealing is applied at different stages of the device manufacturing process.