Hybrid transparent working stamps with both a surface relief and absorbing mask pattern were fabricated by replicating nanostructures in an Ormostamp film on prepatterned glass substrates. By using a combined nanoimprint and photolithography process, self-aligned mixed patterns of nano- and microstructures can be generated within one single resist layer. In this article the authors present a simple process based on the organic-inorganic hybrid polymer Ormostamp by replication on prepatterned Borofloat substrates. Using these working stamps, grating arrays with 35 nm half pitch were replicated in thermoplastic UV-curable resist. The method is easy to employ for generating mesas with nanostructures on top or the backfilling with microstructures in thermal nanoimprint lithography applications.