Methods and systems for setting up a wafer inspection process using programmed defects are provided. One method includes altering a design for a dummy area of a production chip such that printing of the dummy area on a wafer results in printing of a variety of defects. Two or more of the defects have different types, one or more different characteristics, different contexts in the design, or a combination thereof. The dummy area printed on a wafer may then be scanned with two or more optical modes of an inspection system to determine which of the optical mode(s) are better for defect detection. Additional areas of the wafer may then be scanned with the optical mode(s) that are better for defect detection to determine noise information. The noise information may then be used to select one or more of the optical modes for use in a wafer inspection process.