Using Lorentz transmission electron microscopy we investigate the behavior of domain walls pinned at non-topographic defects in Cr(3 nm)/Permalloy(10 nm)/Cr(5 nm) nanowires of width 500 nm. The pinning sites consist of linear defects where magnetic properties are modified by a Ga ion probe with diameter ~ 10 nm using a focused ion beam microscope. We study the detailed change of the modified region (which is on the scale of the focused ion spot) using electron energy loss spectroscopy and differential phase contrast imaging on an aberration (Cs) corrected scanning transmission electron microscope. The signal variation observed indicates that the region modified by the irradiation corresponds to ~ 40-50 nm despite the ion probe size of only 10 nm. Employing the Fresnel mode of Lorentz transmission electron microscopy, we show that it is possible to control the domain wall structure and its depinning strength not only via the irradiation dose but also the line orientation.