In this paper, we demonstrate an extremely efficient technique of diagnosing dengue virus non-structural protein (NS1) using Micro-Spot with Integrated Pillars (MSIP). Detection using MSIP is performed by employing fluorescence immunoassay specific to dengue virus NS1. MSIPs are chemically modified to ensure efficient covalent binding of antibodies on the micropillars, whereas the enormous increase in the surface area (available for the reaction) induced by the micropillars amplifies the apparent rate, which enhances the signal intensity. Therefore, the detection response of a MSIP, quantified by the intensity of the fluorescence signal, is found to be almost five times magnified than the response of a similar size micro-spot without micropillars. The response of the micropillars also depend on the pillar arrangement, since for identical concentration of dengue NS1 antigen, a stronger intensity signal is obtained for a hexagonal close packed array (staggered) pillar arrangement as compared to a square array arrangement.