The competitiveness of algae as biofuel feedstock leads to the growth of membrane filtration as one of promising technologies for algae harvesting. Nanofiber membrane (NFM) was found to be efficient for microalgae harvesting via membrane filtration, but it is highly limited by its weak mechanical strength. The main objective of this study is to enhance the applicability of nylon 6,6 NFM for microalgae filtration by optimizing the operational parameters and applying solvent vapor treatment to improve its mechanical strength. The relaxation period and filtration cycle could be optimized to improve the hydraulic performance. For a cycle of 5 min., relaxation period of ≤2 min shows the highest steady-state permeability of 365 ± 14.14 L m−2 h−1 bar−1, while for 10 min cycle, 3 min. of relaxation period was found optimum that yields permeability of 402 ± 34.47 L m−2 h−1 bar−1. The treated nylon 6,6 NFM was also used to study the effect of aeration rate. It is confirmed that the aeration rate enhances the steady-state performance for both intermittent and continuous mode of aeration. Remarkably, intermittent aeration shows 7% better permeability than the full aeration for all tested condition, which is beneficial for reducing the total energy consumption.