Microfluidics is an emerging technology for buffer exchange in bioprocessing applications. However, achieving buffer exchange with simplicity of operation and high throughput in a straightforward channel design remains a challenge. This study presents a novel semicircular microchannel design that allows for the deterministic regulation of helical and Dean vortices through geometric confinement. By incorporating micro-obstacles into semicircular microchannels with large dimensions (900 μm wide and 100 μm high), we observe a substantial enhancement in secondary flows, leading to a unique fluid distribution across a wide range of flow rates. This design enables a high particle separation efficiency (>96.27%) coupled with a low fluorescein purity (<4.46%) at a high throughput of 3 × 106 particles/min. The proposed methodology, characterized by ease of production (simple semicircular microchannels with large dimensions), user-friendly operation (uniform flow rates in both sheath and sample inlets), and efficient buffer exchange capabilities (typically 3 mL min–1), demonstrates significant potential for advancing microfluidic systems in biological and biomedical research.