A novel PDMS microfluidic spotter system has been developed for the patterning of surface microarrays that require individually addressing each spot area and high probe density. Microfluidic channels are used to address each spot region and large spot arrays can be addressed in parallel. Fluorescence intensity measurement of dye-spotted samples compared to control and pipetted drops demonstrated a minimum of a three-fold increase in dye surface density. This novel spotter system can be applied to the production high-throughput arrays in the fields of genomics, proteomics, immunoassays and fluorescence or luminescence assays.