In this paper, we report a uniform microtrench array fabricated on silicon substrate. The proposed system is aimed for the biological molecules separation process via filtration in artificial kidney. The system consists of silicon based membrane having arrays of trench with the dimension of approximately 1 μm. The fabrication of the trenches is following standard silicon MEMS process with additional surface modification of the fabricated trench by using thermal oxidation process. The result shows that trench patterns having size of 1~2 μm have been produced. The thermal oxidation process shows that the trench size could be reduced up to 50%. The study will be beneficial for the development of silicon membrane with uniform microtrench arrays for application in filtration of blood cell from other solutes based on molecule size. When the microtrench is etched through the silicon membrane, a filtration membrane is then formed. The separation of solutes will be better due to the uniform size of microtrench.