Provided are a programmable mask for promptly fabricating a biomolecule or polymer array having high density, an apparatus for fabricating a biomolecule or polymer array including the mask, and a method of fabricating a biomolecule or polymer array using the programmable mask. The programmable mask for fabricating a biomolecule array or polymer array includes a first substrate including a black matrix having openings and first pixel electrodes; a second substrate including thin film transistors for switching pixel regions which correspond to the openings according to applied electric signals and second pixel electrodes connected to drain electrodes of the thin film transistors; a liquid crystal layer interposed between the first substrate and the second substrate, the liquid crystal layer including liquid crystal whose arrangement can be changed according to electric signals of the thin film transistors so as to selectively transmit light; a first polarizing plate laminated on one side of the first substrate; a second polarizing plate laminated on one side of the second substrate; and a lens array layer laminated on one side of the second polarizing plate including lenses which correspond to the pixel regions.