Early disease diagnosis improves patient outcomes and lowers overall medical costs, but is limited by the need for sensitive diagnostic technology that can detect the earliest possible biological transformation processes. Protein biomarkers are used as diagnostic targets (analytes), but are dilute in the complex milieu of human blood. Separating biomarkers from the background and enriching them to easily detectable concentrations will overcome this issue. Microscale diagnostic technologies have been employed, especially in distributed diagnostic and home healthcare technologies, with great success to address this need. Microscale technologies reduce sample volumes and ease fluid handling constraints, while providing modularity. The vast majority of the molecular components employed in these technologies have remained constant and an opportunity exists to develop new molecular tools to address inherent issues. Current technologies rely on traditional chromatographic techniques that suffer from poor diffusion of large biomarkers and limited activity of surface bound capture moieties. We have developed a series of stimuli-responsive "smart" molecular conjugates that separate and enrich biomarkers from solution and enable detection. Because smart conjugates bind biomarkers in solution prior to separation, conjugate-biomarker binding avoids steric and mass transport limitations associated with surface-based techniques. We have also developed "smart" surfaces that trap and release smart conjugates in microscale devices. In this work we incorporated "smart" conjugates and surface traps into a modular microscale diagnostic platform for the quantitation of disease biomarker concentration in biologically complex solutions. Prostate Specific Antigen (PSA) has been used as a model biomarker to validate microsystem modularity. We have combined molecular design of sophisticated bioconjugates with advanced microfluidic flow and mixing technologies to develop a novel system for protein biomarker separation and enrichment.