Advances in microfabrication technologies have enabled the production of high precision, low cost and high performance micro systems. Microchannels are widely used in microfluidic and nanofluidic applications, such as microelectromechanical, chemical and biological devices, as one of the basic components of micro systems. Various microfabrication methods have been developed depending on the material of microchannels, dimensional accuracy, surface structure, desired mechanical and thermal properties. In general, it can be said that these production methods are based on precision mechanical manufacturing, silicon-based fabrication and polymer processing technologies. However, in order to achieve the desired precision and quality in micro-scale productions, it is necessary to make some changes in these manufacturing techniques. It is not possible to obtain products with the desired properties in both macro and micro scale by using the same process in most fabrication methods. In this study, the size and surface characteristics of microchannel heat sinks obtained with different manufacturing techniques for use in heat transfer and flow process were compared. Microchannel heat sinks are manufactured using lithography, precision mechanical processing, laser-based production methods, electro-erosion processing methods. Metrological characterization of the microchannels obtained were made with an optical microscope and an optical profilometer. The microfabrication methods used have been evaluated in terms of achieving the same production tolerance for each microchannel, having micro-channels rectangular profile, radius formation at the microchannel base, controlling the surface roughness value and having a homogeneous roughness distribution of the surface. It has been observed that the method that best meets these criteria is microchannel heat sinks manufactured by sinking electro-erosion technique.