The addition of structural defects modifies the intrinsic properties of graphene–the two dimensional allotrope of carbon. The controlled introduction of such defects is therefore desired to realise specific functions. For instance, the grain boundaries formed between epitaxial grown graphene domains has been observed to mimic a metallic wire. By contrast, the presence of point defects in a graphene channel affects the carrier transport significantly in a manner such as the Fermi-level pinning, transport-gap widening and Anderson localization. Incorporating these defects into conventional device structures can open up a new horizon for device engineering. In this work, I propose and explore the defect engineering of graphene devices via ion bombardment using a helium ion microscope (HIM). The lithographic advantage of HIM is demonstrated for various graphene nanostructures such as fully gated 20nm double quantum dots and 10nm nanoribbons, upon which a hybrid EBL-HIM fabrication technique is developed for device integration. Graphene irradiated with HIM up to 5×1014 cm-2 shows a transition from Stage 1 to Stage 2 disorder as probed by confocal Raman spectroscopy. For the first time, the damage of ion-beam-milling on a graphene-onsubstrate sample is visualised. The spatially resolved Raman map shows that the beam damage can extend to a few hundred nm around the 30nm cut, which is attributed to the damage due to backscattered helium ions and recoils from the substrate. Furthermore, the electrical properties of irradiated graphene nanoribbons (iGNR) is characterised. As irradiation dose increases, the iGNR devices shows an abrupt decrease in mobility and interestingly an asymmetric decrease of conductance in the electron and hole conduction branches. This is then related to the pinning of Fermi level in iGNR, a unique property caused by irradiation. This is believed to be associated with additional dangling bonds (scattering centres) created by irradiation, as supported by XPS analysis. Based on these properties, a new graphene device structure is explored, in which irradiated regions are used as energy barriers. The temperature-dependent conductance shows the signature of thermal-activated variable range hopping (VRH) at intermediate temperature. The localisation lengths extracted from hopping temperature showed good agreement with that from length-dependent conductance. Furthermore, the activationless VRH is observed for relatively high electric field.