Generally, machining of polymeric microfluidic devices is a one-step manufacturing process. It is economical compared to lithography and can be used for batch production and rapid prototyping. However, surface properties are modified during machining due to the viscoelasticity property of polymers and the mechanical nature of fractures. In this present work, the manufacturing capability of the mechanical micromachining process of polymers has been explored. Surface characteristics like surface roughness, surface energy, and burr formation are investigated. Surface quality is chosen as a contributing factor for defining the manufacturing capability as it is one of the significant factors influencing the physics of fluid flow in microchannels. In the present work, several manufacturing methods, such as 3D printing, hot embossing, photolithography, and mechanical micromachining, were considered. The surface energy of various surfaces machined using the abovementioned methods is evaluated and compared. It has been observed that mechanical micromachining is the most suitable methods as they have less wettability with lower surface energy. Further investigations are carried out by machining microfluidic devices using polymethylmethacrylate (PMMA) and polycarbonate (PC) materials, as they are extensively used in biomedical applications. Surface roughness was measured on the PMMA and PC surfaces after milling. The surface roughness values and surface energies are used for evaluating the suitability of the machining process to fabricate microfluidic devices. Microfluidic devices with serpentine channels were machined on PMMA with a depth of 50 µm and width of 200 µm for evaluating inertial focusing in the channels. These devices were further evaluated for blood cell separation at different dilution rates. It is observed that PMMA is the preferable choice for fabricating microfluidic devices using mechanical micro-milling.