An improved optical photolithography system and method provides predetermined light patterns generated by a direct write system without the use of photomasks. The Direct Write System provides predetermined light patterns projected on a surface of a substrate (e.g., a wafer) by using a computer controlled spatial light modulator. Image patterns are stored in a computer and through electronic control of pixels in the spatial light modulator, directly illuminates the wafer to define a portion of the polymer array, rather than being defined by a pattern on a photomask. For example, in the Direct Write System using a micro-mirror array as the spatial light modulator, the angle of each pixel of micro-mirror array is computer controlled to reflect or not reflect an optical beam of suitable intensity to thereby image (printing) individual features on the substrate at each photolithographic step without using a photomask. The Direct Write System including a spatial light modulator is particularly useful for deprotecting features for polymer array synthesis (e.g. synthesis of DNA arrays).