This thesis describes the capabilities of the helium ion microscope (HIM) and that of graphene to explore fundamental physics and novel applications. While graphene offers superior electronic properties, the helium ion microscope allows us to combine imaging and modification of materials at the nanoscale. We used the capabilities of HIM to grow 3D-AFM probes, which can be used in the critical dimension semiconductor metrology. Moreover, we studied the ion-material interactions, needed to enable the fabrication of functional graphene nanoribbons. Similarly, we used the superior electronic properties of graphene to make ballistic Josephson junctions and studied the current-phase relation (CPR) of these junctions.