The computational fluid dynamics (CFD) simulation on the effect of pillar shapes on chitosan-ZnO nanoparticles flows in pillar-based microfilter was considered using ANSYS Fluent in the laminar flow condition. Three shapes of the pillar were studied: cylindrical, cuboid, and rotated cuboid pillar. The volume of fluid (VOF) method was performed under a certain set of considerations and assumptions in order to validate the microfilter design to have the same flow patterns based on the literature. The discrete phase model (DPM) was carried out in order to simulate and analyze the chitosan-ZnO nanoparticles flow behaviour and separation efficiency performance in pillar-based microfilter. The DPM was carried out in 200, 300, and 400 streams to track the position of the nanoparticles in order to analyze the separation performance for each pillar shape. The simulation involved a different number of streams that were observed on the impact of nanoparticle Reynolds number and the total number of nanoparticles. It was observed that microfilter-C (rotated cuboid pillar) has the best separation efficiency of chitosan-ZnO nanoparticles compared to microfilter-A (cylindrical pillar) and microfilter-B (cuboid pillar) based on the particle position from the outlet of microfilter which was 2.5 mm, 0.08 mm, and 2.1 mm respectively. The shape of the pillar is a critical parameter that plays a significant role in the separation performance of nanoparticles in pillar-based microfilter. © 2020 Institute of Physics Publishing. All rights reserved.