Microfluidic devices fabricated through mechanical micromachining techniques have already been reported to be highly economical when compared to other techniques. Direct mechanical machining processes are generally classified as a one-step manufacturing process, having the advantages of rapid prototyping and batch production. Though there are advancements in ultra-precision machining techniques, the real challenge of direct machining polymeric microfluidic channels is the occurrence of poor surface integrity owing to the change in mechanical as well as viscoelastic properties. This forms the key objective of the present research work, where the major emphasis has been given to understand the applicability of micro-milling techniques in fabricating microfluidic devices, especially for bio-applications. In this research, the mechanical micro-milling technique was used to create microscale channels on polymethylmethacrylate (PMMA) and polycarbonate (PC) materials; wherein the process capability was mainly assessed based on the surface characteristics of the micro features. Furthermore, for the quantitative analysis, a comparative study was also performed by measuring the surfaces roughness and surface energy of the microchannels made by various fabrication routes such as hot embossing and lithography. The experimental results indicate that the micro-milling of PMMA is the preferable choice for fabricating microfluidic devices when compared to PC. Also, for showing the manufacturability of the mechanical micromachining technique, microfluidic channels with serpentine channels were machined with a depth and width of 50µm and 200µm respectively. The applicability of the fabricated microfluidic devices was further validated by evaluating the functioning of these devices for blood cell separation at different dilution rates.