Methods and systems for detecting defects on a wafer are provided. One method includes altering one or more design clips based on how the one or more design clips will appear in output generated by a wafer inspection process for a wafer. The method also includes aligning the one or more altered design clips to the output generated for the wafer during the wafer inspection process. In addition, the method includes detecting defects on the wafer based on the output aligned to the one or more altered design clips.