A prepared substrate upon which light directed DNA synthesis is to occur is exposed to light via an inverse mask pattern to deprotect inactive regions of the substrate where the synthesis is not intended to occur. The deprotected sites are then capped to disable permanently the inactive areas, thereby forming an inverse capped substrate. Unwanted DNA synthesis in the inactive areas is thus prevented, resulting in purer quality DNA, even though such areas may be exposed to light due to diffraction, scattering and flare during subsequent DNA synthesis of the intended active areas of the substrate.