Provided are methods for processing a substrate using a proximity system defined by one or more meniscus windows on one or more proximity heads. One method includes applying a first fluid meniscus to a surface of the substrate to apply a chemical precursor to the surface of the substrate. The first fluid meniscus is applied to first proximity meniscus window. Then, applying a second fluid meniscus to the surface of the substrate to leave an atomic layer of the chemical precursor on the surface of the substrate, through a second proximity meniscus window. A third fluid meniscus is applied to the surface of the substrate to apply a chemical reactant configured to react with the atomic layer of the chemical precursor to generate a layer of a material, through a third proximity meniscus window. The first, second and third proximity meniscus windows are arranged to apply the first fluid meniscus, the second fluid meniscus and the third fluid meniscus one after the other to a same location of the surface of the substrate during movement of the substrate through the proximity system.