Optical waveguides are one of the most important photonic components. They are indispensable tools in many of today’s technologies because of their capacity of guiding light. In particular, compact, low loss, flexible polymer optical waveguides are crucial in optofluidic and microfluidic devices for a dense integration of optical functionalities. The sought after suitable materials and innovative fabrication techniques to achieve low loss long polymer optical waveguides and interconnects has proven to be challenging. In a fiber optic endoscope, thousands of single-mode (SM) optical fibers acting as single pixels are closely packed together, delivering the local information to a camera chip. Biocompatible polymer-based waveguides increasingly became valid alternatives to silica fibers to deliver and collect light for optical diagnosis, therapy and surgery. In particular, polydimethylsiloxane (PDMS) is well known to be a suitable polymer for biomedical implantation devices, thanks to its excellent physical and chemical properties. In this thesis, I demonstrate the fabrication of compact optical waveguides in PDMS through multiphoton laser direct writing (MP-LDW). The core of this research consists of the investigation of suitable combinations of monomer and PI capable of efficient photopolymerization in a cured PDMS matrix. We achieved, for the first time, the photoinitiator-free fabrication of optical waveguides employing phenylacetylene as the photosensitive monomer via multi-photon absorption. Because of the dense π-electrons in phenylacetylene, we achieved a high refractive index contrast (Δn ≥ 0.06) between the waveguide core and the PDMS cladding. This allowed for efficient waveguiding at a core size of 1.3-µm with a measured loss of 0.03 dB/cm in the spectral band of 650-700 nm. Motivated by the need of minimizing self-focusing, we investigated alternative chemical schemes and demonstrated the fabrication of submicron optical waveguides in PDMS using divinylbenzene (DVB) as the monomer through two-photon polymerization (2PP). We show that the commercial oxime ester photoinitiator Irgacure OXE02 is suitable for triggering the DVB polymerization, resulting in a stable and controllable fabrication process for the fabrication of defect-free, 5-cm long waveguides. Moreover, I present the methodologies we have developed for the fabrication of polymer rectangular step-index (STIN) optical waveguides using a commercial 3D printing system (Photonic Professional GT, Nanoscribe GmbH), using the proprietary IP-dip resist. We performed a full calibration and implemented a printing strategy for the fabrication of a 720 ÎŒm long SM-fiber bundle. We characterized it in terms of refractive index, transmission loss and imaging capabilities. We further demonstrate how a convolutional neural network (CNN) can reconstruct the original images from a scrambled output from the waveguide bundle due to crosstalk. To achieve this, we have constructed a CNN of the U-net type and trained the network with the input images and their corresponding output from the bundle. Overall, the presented work provides innovative materials and new insights into the fabrication of polymer optical microstructures, opening new scenarios for future technological development in the field of microfabrication using MP-LDW. We expect such waveguides will receive a wide range of applications in biosensors, microfluidic flow cytometry and wearable photonic devices.