A method for preparing a glass surface containing an ordered array of nanowells is described. These nanowell arrays are prepared via a plasma-etch method using a nanopore alumina film as the etch mask. A replica of the pore structure of the alumina mask is etched into the glass. We demonstrate that chemical information in the form of negatively charged latex nanoparticles can be selectively stored within these nanowells and not indiscriminately deposited on the surface surrounding the nanowells. To accomplish this, the chemistry of the glass surfaces within these nanowells (walls and bottoms) must be different from the chemistry of the surface surrounding the nanowells. Two different procedures were developed to make the inside vs. surrounding surface chemistries different. Atomic force microscopy (AFM) was used to image the nanowells and, via friction-force measurements, to prove that the inner nanowell surfaces can be made chemically different from the surface surrounding the nanowells.