Microfluidics finds a wide range of industrial applications mainly in fields such as biomedical, clinical, electrical, and thermal engineering. Microchannels are the building blocks of most microfluidic devices. Thus, it becomes evident to understand the properties and the effect of the surfaces on the outcomes of devices. In this study, the effect of the shape of microchannels and the roughness elements on the flow is evaluated. Microchannels with three cross-sections and roughness elements of three different geometries are considered. The effect of varying Reynolds numbers on the flow parameters such as Friction factor, Nusselt number, Poiseuille number, pressure drop and surface temperature at the base of the substrate is studied. It is observed that rough microchannels and rectangular roughness elements showed a higher Nusselt number than smooth microchannels. The rough microchannels with triangular roughness elements showed higher friction factors. The surface temperature is higher for the smooth microchannels with triangular roughness elements. Furthermore, to demonstrate the manufacturability of microfluidic channels with controlled surfaces and to validate the preliminary results of the numerical simulations, the ultrashort pulse laser micromachining technique is used to fabricate the microchannels with structures on Polymethyl Methacrylate (PMMA) material.