Nanoimprint lithography (NIL) has been established as a high-throughput technique to fabricate sub-25-nm patterns at a low cost. The fabrication of NIL templates with features in the submicrometer range is currently a bottleneck of the NIL technology. The replication of errors on NIL templates places a major challenge on the reusability of templates. Focused ion beam (FIB) technology is employed to modify prestructured NIL templates. In this work, repair strategies for NIL stamps are discussed. Excess material from stamps has been removed by ion milling. Nanoscale trenches and ultrathin lamellas fabricated with a focused ion beam and their corresponding imprints are presented. It has been confirmed that commercial UV-NIL stamps can be modified by FIB milling and imprinted line patterns were successfully replicated by UV-NIL using the repaired templates. Furthermore, the potential of three-dimensional NIL templates structured by FIB was evaluated. Three-dimensional imprints with features down to 80 nm with good structure conformity to the template were demonstrated. The capabilities and limitations of FIB as repair technology for NIL stamps are discussed.