The present invention provides substrates having a plurality of micro-locations on its surface. Each micro-location has an effective dose of an ion beam treatment such that the plurality of the micro-locations exhibit an affinity to a compound that is different from the affinity of the remainder of the substrate surface to that compound. The substrates of the invention can be utilized to form microarrays of biological molecules, such as oligonucleotides or peptides. Such microarrays can find a variety of applications. For example, they can be employed in large scale hybridization assays in many genetic applications, such as mapping of genomes, monitoring of gene expression, DNA sequencing, genetic diagnosis, and genotyping of organisms.