Microelectromechanical systems (MEMS)-based filter with microchannels enables the removal of various microorganisms, including viruses and bacteria, from fluids. Membranes with porous channels can be used as filtration interfaces in MEMS hemofilters or mini-dialyzers. The main problems associated with the filtration process are optimization of membrane geometry and fouling. A nanoporous aluminum oxide membrane was fabricated using an optimized two-step anodization process. Computational strength modeling and analysis of the membrane with specified parameters were performed using the ANSYS structural module. A fuzzy simulation was performed for the numerical analysis of flux through the membrane. The membrane was then incorporated with the prototype for successive filtration. The fluid flux and permeation analysis of the filtration process have been studied. Scanning electron microscope (SEM) micrographs of membranes have been obtained before and after the filtration cycles. The SEM results indicate membrane fouling after multiple cycles, and thus the flux is affected. This type of fabricated membrane and setup are suitable for the separation and purification of various fluids. However, after several filtration cycles, the membrane was degraded. It requires a prolonged chemical cleaning. High-density water has been used for filtration purposes, so this MEMS-based filter can also be used as a mini-dialyzer and hemofilter in various applications for filtration. Such a demonstration also opens up a new strategy for maximizing filtration efficiency and reducing energy costs for the filtration process by using a layered membrane setup.