Microarray analysis as a tool that provides the opportunity for simultaneous study of thousands of molecules has greatly contributed to research in many areas including functional genomics and proteomics, disease diagnosis and drug discovery. Pin-based spotting has been widely used in microarray fabrication. This paper investigates blotting procedure, that is, removing excess reagent from pins. A new optimum blotting pattern is proposed. Blotting constraints and parameters are identified and a new pattern, Beta program is proposed and compared with a patented and commonly used blotting pattern, Alpha program. A simulation program has been developed using LabVIEW to demonstrate and compare different blotting patterns. Based on the simulation results, the optimal blotting pattern in terms of speed of blotting operation and density of spots on a slide using different types of source microplates has been obtained. The optimum Beta program showed an increase of 11 times in the density of spots compared to the Alpha program. The Beta program is ready for implemention to improve the efficiency of blotting procedure.