Ramp-edge YBa2Cu3/PrBa2Cu3Ox/YBa2Cu3Ox Josephson junctions with PrBa2Cu3Ox (PrBCO) or SrTiO3 as a separating layer on different kinds of substrate have been studied by high-resolution electron microscopy. The bottom YBa2Cu3Ox (YBCO) layer and the separating layer (PrBCO or SrTiO3) were epitaxially c oriented, irrespective of the substrate (yttria stabilized zirconia (YSZ), SrTiO3 or NdGaO3, all in (001) orientation). The use of ion milling in the manufacturing of Josephson junctions was found to yield smooth slopes with an angle of about 20°. The Josephson junction was facing away from the beam direction was found to have a dimple in the substrate near the base of the junction. The barrier layers were observed to have a homogeneous thickness. These layers were as the top YBCO layers were oriented with their c-axis perpendicular to (001) plane of the substrate for perovskite substrates and perpendicular to the surface for YSZ substrates. In the case of a YSZ substrate, the dimple in the substrate as well as the slope of the substrate close to the base of the junction were found to lead to small angle grain boundaries in the YBCO film as well as randomly oriented YBCO grains, which results in a poor ramp-edge junction. In the case of SrTiO3 or NdGaO3 substrate, all components of the device were fully epitaxial, thus resulting in good ramp-edge junctions.