An inherent problem with microfluidic filters is the tendency to clog, especially when applied to cells due to their geometrical complexity, deformability, and tendency to adhere to surfaces. In this work, we handle live algal cells of high complexity without signs of clogging, achieved by exploiting hydrodynamic interactions around trilobite-shaped filtration units. To characterize the influence of cell complexity on the separation and concentration mechanisms, we compare the hydrodynamic interactions to those of synthetic, rigid microparticles. We discover that simple rolling along the filter structures, which prevents clogging for particles, cannot be applied to cells. Instead, we find that inertial effects must be employed to minimize the filter interactions and that this modification leads to only a minor reduction in device performance.