Using a focused ion beam microscope we have created non-topographic features that provide controlled modification of domain wall structure, size and pinning strength in 500nm wide nanowires composed from Cr(3 nm)/Permalloy(10 nm)/Cr(5 nm). The pinning sites consist of linear defects where magnetic properties were modified by a Ga + ion probe of diameter ~ 10 nm. Detailed studies of the structural, chemical and magnetic changes induced by the irradiation, which showed the modified region to be ~40-50nm wide, were performed using scanning transmission electron microscopy modes of bright field imaging, electron energy loss spectroscopy and differential phase contrast imaging on an aberration (Cs) corrected instrument. The Fresnel mode of Lorentz transmission electron microscopy, was used for studies of domain wall behaviour, where we have observed changes in depinning strength and structure with irradiation dose and line orientation. We present an understanding of this behaviour based upon micromagnetic simulation of the irradiated defects and their effect on the energy terms for the DWs.