Microalgae species have great economic importance; they are a source of medicines， health foods， animal feeds， industrial pigments， cosmetic additives and biodiesel. Specific microalgae species collected from the environment must be isolated for examination and further application， but their varied size and culture conditions make their isolation using conventional methods， such as filtration， streaking plate and flow cytometric sorting， labour-intensive and costly. A separation device based on size is one of the most rapid， simple and inexpensive methods to separate microalgae， but this approach encounters major disadvantages of clogging and multiple filtration steps when the size of microalgae varies over a wide range. In this work， we propose a multilayer concentric filter device with varied pore size and is driven by a centrifugation force. The device， which includes multiple filter layers， was employed to separate a heterogeneous population of microparticles into several subpopulations by filtration in one step. A cross-flow to attenuate prospective clogging was generated by altering the rate of rotation instantly through the relative motion between the fluid and the filter according to the structural design of the device. Mixed microparticles of varied size were tested to demonstrate that clogging was significantly suppressed due to a highly efficient separation. Microalgae in a heterogeneous population collected from an environmental soil collection were separated and enriched into four subpopulations according to size in a one step filtration process. A microalgae sample contaminated with bacteria and insect eggs was also tested to prove the decontamination capability of the device.