Biofuel is one of the renewable energy resources alternatives to fossil fuels . Among various sources for biofuels, microalgae provide at least three-orders-of-magnitude higher production rate of biodiesel at a given land area than conventional crop-based methods. However, microalgal biodiesel still suffers from significantly lower harvesting performance, making such a fuel less competitive. To increase the separation performance of microalgae from cultivation solution, we used a spiral microchannel that enables the isolation of biofuel-algae particles from water and contaminants contained in the culturing solution. Our preliminary data show that separation performance in the microfluidic centrifugal separator is as high as 88% within a quick separation time of 30 seconds. To optimize separation performance, multiple parameters of algae behaviors and separation techniques were studied and were manipulated to achieve better performance. We found that changing these factors altered the separation performance by increasing or decreasing flocculation, or “clumping” of the microalgae within the microchannels. The important characteristics of the separator geometry, fluid properties, and environmental conditions on algae separation was found and will be further studied in the forthcoming tests. This introductory study reveals that there is an opportunity to improve the currently low performance of algae separation in centrifugal systems using much smaller designs in size, ensuring a much more efficient algae harvesting.