In a process for patterning both sides of a double-sided HTS thin film wafer with the patterns in close registration, the first side is patterned with at least one reference mark and the second side is patterned with at least one aperture which permits alignment of the reference mark from the already applied pattern on the first side preferably to a similar reference mark on the yet to be applied patterns on the second side, such that the patterns can be aligned in close registration, using microcopic viewing techniques if necessary.