Research into the development of advanced RF electronics and devices having high-Temperature Superconducting (HTS) circuitry is being carried out in the Cryogenic Exploitation of RF (CERF) laboratory at SPAWAR Systems Center (SSC) -Pacific. Recently, we have developed a novel annealing process wherein a film of YBa 2 Cu 3 O x is produced having a gradient of oxygen composition along a given direction which we refer to as YBa 2 Cu 3 O ∇x . Such samples are intended for rapid experimental investigation of the evolution of electronic properties within the compound and in combination with structurally compatible functional oxide materials as integrated sensor devices. We present here an investigation as to the extent to which local oxygen content affects the ion milling process in the formation of Josephson junctions in the HTS compound YBa 2 Cu 3 O ∇x . We find an abrupt transition in the profile and depth of ion milled trenches at oxygen concentrations at and below the well ordered oxygen level, O 6.72 . The method described here shows good potential for use in the fabrication of large numbers of uniform Josephson junctions in films of YBa 2 Cu 3 O x , as either a complementary processing tool for grain boundary, step edge, or ion damaged formed JJs, or as a stand alone method for producing nano-bridge JJ's.