We studied the microstructure of Ar ion-beam etched ramps in epitaxial DyBa2Cu3O7-d films by atomic force microscopy. Generally, ramps were well aligned with one of the crystal axes of the (001) SrTiO3 substrate. In those cases we observed a surface reconstruction into a regular pattern of very long (up to 0.5 mm), about 20 nm wide facets, parallel to the ramp edge. For high misorientation angles, the reconstruction appeared much more complex and less regular. Furthermore, we investigated the nucleation and growth of very thin barrier layers of PrBa2Cu3O7-d on well aligned ramps. We found that nucleation takes place in the shallow trenches in the ramp, where facets meet. When more material is deposited, islands coalesce to form closed domains parallel to the trenches. This causes a thickness modulation close to 100% for barrier layer thickness up to 6 nm. The conclusions drawn from this research allow for an important improvement of the technology for the fabrication of ramp-type junctions.