Nominally identical permalloy nanowires, with widths down to 150 nm, were fabricated onto a single-electron transparent Si3 N4 membrane using electron beam lithography (EBL) and focused ion beam (FIB) milling. Transmission electron microscopy (TEM) experiments were performed to compare the nanostructures produced by these two techniques in what we believe is the first direct comparison of fabrication techniques for nominally identical nanowires. Both EBL and FIB methods produced high quality structures with edge roughness being of the order of the mean grain size 5–10 nm observed in the continuous films. However, significant grain growth was observed along the edges of the FIB patterned nanowires. Lorentz TEM in situ imaging was carried out to compare the magnetic behavior of the domain walls in the patterned nanowires with anti-notches present to pin domain walls. The overall process of domain wall pinning and depinning at the anti-notches showed consistent behavior between nanowires fabricated by the two methods with the FIB structures having slightly lower characteristic fields compared to the EBL wires. However, a significant difference was observed in the formation of a vortex structure inside the anti-notches of the EBL nanowires after depinning of the domain walls. No vortex structure was seen inside the anti-notches of the FIB patterned nanowires. Results from micromagnetic simulations suggest that the vortex structure inside the anti-notch can be suppressed if the saturation magnetization (Ms) is reduced along the nanowire edges. A reduction of Ms along the wire edges may also be responsible for a decrease in the domain wall depinning fields. Whereas the two fabrication methods show that well-defined structures can be produced for the dimensions considered here, the differ- - ences in the magnetic behavior for nominally identical structures may be an issue if such structures are to be used as conduits for domain walls in potential memory and logic applications.