In mask-alignment systems a reference signal is needed to align the mask with the silicon wafers. The optical reference signal is the autocorrelation of two two-dimensional (2D) codes with binary transmittance. For a long time, one-dimensional codes have been used in grating-measurement systems to obtain a reference signal. The design of this type of code has needed a great computational effort, which limits the size of the code to about 100 elements. Recently, we have applied genetic algorithms to design codes with arbitrary length. We propose the application of these algorithms to design 2D codes to generate 2D optical signals used in mask-alignment systems.