A peristaltic pump-based apparatus for capturing circulating tumor cells (CTCs) from blood is provided that includes a feedback control architecture that uses models of pump operation and measures of internal pressure fluctuations of the pump (e.g., in the form time-varying and/or position-dependent pressure oscillation data) to adjust pump operating characteristics that smooth pump operation, thereby improving viscosity and consistency of fluid flowing through the pump to a connected microfluidic capture device.