Microscale optofluidic devices are a category of microscale devices combining fluidic and optical features. These devices typically enable in-situ fluid flow measurement for pharmaceutical, environmental or biomedical applications. In micro-optofluidic devices, in order to deliver, as close as possible, the input light to the sample or a specific chip section and, collect the output signal, it is necessary to miniaturize optical components. In this paper, two low-cost technologies, 3D Printing PDMS-based and laser cutting PMMA-based (PDMS stands for Poly-dimethyl-siloxane and PMMA for Poly-methyl-methacrylate), were investigated as novel methods to realize micro-optical waveguides (μWGs) comparing their performances. An ad-hoc master-slave protocol developed to realize PDMS components by 3D Printing has been fully optimized. The manufacturing technologies proposed require simple and low-cost equipment and no strictly controlled environment. Similar results are obtained for both the micro-optical waveguides realized. Their losses, disregarding the losses caused by the fibers’ alignment and the miss-match of the geometry with the waveguide, are of the order of 20%, almost equivalent for both approaches (PDMS-μWG and PMMA-μWG). The losses are of the order of 10% when the PDMS-μWG is shielded by a copper layer, with a significant improvement of the signal acquired. The results obtained show the possibility of using the two low-cost technologies presented for the realization of micro-optical waveguides suitable to be integrated in micro-optofluidic devices and the potential of creating micro-optical paths inside micro-embedded systems.