This paper presents a design and fabrication of a fluid filtration system for separating biological molecules through uniform pores in silicon-based planar microfiltration system. The study is aimed to find a simple process for the fabrication of a microfiltration system. The uniform pores are made of aluminium (Al) material deposited on a silicon substrate, whereas the fluid chamber is fabricated using deep reactive ion etching (DRIE) process of the substrate by utilising SF6 as the reaction gas. Afterwards, the prepared filtration membrane is directly bonded with PDMS based microfluidic part using a corona discharge. Tygon S3™ tubings are used as the fluid interconnection between the PDMS sealing layer and the silicon-based Al membrane in order to make up complete silicon-based planar microfiltration system with uniform pores for separating molecules in fluid based on molecule size. The silicon-based planar microfiltration system consists of assembled siliconbased Al membrane, PDMS sealing layer and Tygon tubes. From the initial test conducted, no leaking is detected from the PDMS sealing, and the initial test using DI water shows that the DI water can flow through the uniform filtration pores. The silicon-based planar microfiltration system with uniform pores has the potential to be used in the filtration of biological fluid in separating molecules based on size.