Early diagnosis of prostate cancer and evaluation of appropriate treatment options requires development of effective and high-throughput selective capture technology for exosomes that are positive for the expression of enzyme-biomarker, prostate-specific membrane antigen (PSMA). Exosomes are small secreted vesicles that play a key role in intercellular communication and cancer progression. PSMA is highly enriched in exosomes excreted by PSMA+ prostate cancer cells. Using PSMA+ cells from the well-established prostate cancer cell line (LNCaP), the secreted exosomes were collected and isolated from the culture medium. The tumor-derived exosomes were selectively captured using a novel silica nanostructure support that had been functionalized with the small-molecule ligand TG97, a known inhibitor of PSMA enzymatic activity that binds irreversibly in the active site of PSMA. The concept was demonstrated using a single cancer type (i.e., prostate cancer), but based on the data obtained the approach may be applicable to a broad panel of biomarker ligands for selective capture of biomarker-positive exosomes from an array of cell types. The approach demonstrated herein overcomes many of the limitations of alternative methods that are often ineffective in isolating tumor-derived exosomes from those derived from normal tissue because of the low yield recovery and the time required for the process. A further advantage is the ability to isolate a specific subpopulation of exosomes relying on the expression of a specific surface marker as well as improved exosome recovery rate.