For many years, the development of effective ablation or laser machining techniques for making micro-optical components has been the key factor in the birth of new photonic devices and systems. In this article, the ablation characteristics of two types of the most important transparent materials, transparent polymers and glasses, are studied. Simple shaped microcavities are first machined for studying the fundamental ablation parameters, including threshold fluence, effective absorption coefficient, and ablation rate. In studying polymer ablation, five standard grades and five proprietary polymeric compounds are selected. Ablation techniques using these transparent polymers for making arrayed ferrules and curved microlenses are presented. Applications of these ablated microstructures for optical fiber connectors, optical fiber coupling and alignment, and transparent chip encapsulants, are introduced and demonstrated with emphasis on the quality of the ablated profiles and dimensions to satisfy the required performance. In glass ablation, borosilicate glasses are considered and their associated ablation behaviors are studied. The procedures to ablate glass-based arrayed microstructures with flat and curved surfaces are described. The utilizations of these arrayed microstructures for optical waveguide, wave absorber, and beam guider, are specifically discussed. Finally, concluding remakes for future trends are presented.