the other features in fig3 such equipment may or may not be located at the same physical site but is shown together for ease of illustration in fig3 the system 106 generates masks 110 or other synthesis patterns such as chrome on glass masks for use in the fabrication of polymer arrays the masks 110 as well as selected information relating to the design of the chips from system 100 are used in a synthesis system 112 synthesis system 112 includes the necessary hardware and software used to fabricate arrays of polymers on a substrate or chip 114 for example synthesizer 112 includes a light source 116 and a chemical flow cell 118 on which the substrate or chip 114 is placed mask 110 is placed between the light source and the substrate chip and the two are translated relative to each other at appropriate times for deprotection of selected regions of the chip selected chemical regents are directed through flow cell 118 for coupling to deprotected regions as well as for washing and other operations all operations are preferably directed by an appropriately programmed computer 119 which may or may not be the same computer as the computer s used in.