Atomic Layer-by-Layer Molecular Beam Epitaxy (ALL-MBE) of high Tc superconducting films can be used to grow defect-free and flat multi-layer structures in which superconducting molecular layers are stacked with molecular layers having other electronic properties. In particular, tri-layers consisting of c-axis Bi2Sr2CaCu2O8 base and counter electrode layers, each several hundred angstroms thick, have been grown separated by single molecular layers of metastable compounds such as Bi2Sr2Can-1CunO2+4 where n ranged from 5 to 11. Furthermore, the electronic properties of such barrier layers have been modified by doping with trivalent cations. Using such structures, tri-layer Josephson junctions have been fabricated which exhibit hysteretic I - V characteristics. Other doping schemes have given insulating layers which dominate c-axis transport, demonstrating the ability of this technique to grow thin, 25 Å, single molecular layers that are free of pinholes.