To improve diffusive capabilities and target accessibility with a gel-based microarray, a novel 'pads within a pad' approach was developed. Using a soft lithography technique, an array of 'waffle'-like micro-pillars embedded on the surface of the glass slide substratum was fabricated. The micro-pillar based microarray showed more than a 3-fold increase in the effective surface area available for probe immobilization. As a result, a 5-fold increase was observed in the hybridization rate and intensity of the 'waffle' pad as compared to an unmodified gel pad. The functionality of the 'waffle' pad was demonstrated by the accurate genotyping of two sets of SNPs (SNP_1236 and SNP_2677) based on the dissociation curve, dissociation temperature, Td and the difference of Td between the perfect match duplex with that of the mismatch (ΔT d).