A particle separation multi-membrane matrix device and method are provided. The particles isolated may comprise nano-scale particles, such extracellular membrane vesicles, having a size of about 50 to about 150 nm. The vesicles are released by many different cell types, and may be efficiently isolated at high yield and purity according to the present methods from various body fluids (e.g., blood, saliva, breast milk, serum, plasma, ascites fluid, etc.). Such isolated exosome preparations may include biomarkers, such as disease biomarkers (diagnostic markers) for various disease (early stage and late stage cancers, neurological disorders (Parkinson disease, Alzheimer disease), diabetes, pancreatic diseases, renal failure, infectious diseases (HIV, tuberculosis, malaria, hepatitis)). The present methods and devices may be used to detect and monitor animals (human, livestock, companion animal) for infectious diseases, such as tuberculosis and other diseases. The methods and devices require minimal sample material (10 μl), are rapid, economical, yield highly enriched small molecule (eg, exosomes) preparations, and do not require electricity.