Since the discovery of the unconventional copper-oxide high-transition-temperature superconductors (HTS), researchers have explored many methods to fabricate superconducting tunnel junctions from these materials for both superconducting electronics operating at the practical temperature of liquid nitrogen (77 K) and for fundamental measurements essential for testing and guiding theories of these remarkable superconductors. The difficulty is that the traditional estimate of the superconducting coherence length is very short and anisotropic in these materials, typically ~2 nm in the a-b plane and ~0.2 nm along the c-axis. The coherence volume encloses very few superconducting pairs, so even the presence of small scale inhomogeneities can locally disrupt superconductivity unlike in conventional superconductors. Therefore the electrical properties of Josephson junctions are sensitive to chemical variations and structural defects on atomic length scales, thus to make multiple uniform HTS junctions, control at the atomic level is required. In this letter, we demonstrate very high-quality all-HTS Josephson superconducting tunnel junctions (both Josephson and quasiparticle tunneling) created by using a 500 pm diameter focused beam of helium ions to direct-write tunnel barriers into YBa2Cu3O7(YBCO) thin films. With this method we demonstrate the ability to control the barrier properties continuously from conducting to insulating by varying the irradiation dose. This technique provides a reliable and reproducible pathway for the scaling up of quantum mechanical circuits operating at practical temperatures (~77 K) as well as an avenue to conduct superconducting tunneling studies in HTS for basic science.