Laser machining is an inexpensive and fast alternative to conventional microfabrication techniques and has the capability to produce complicated three-dimensional (3D), hierarchical structures. It is especially important while performing rapid prototyping and quick design studies of extreme heat flux cooling devices. One of the major issues plaguing the use of laser micromachining to manufacture commercially usable devices, is the formation of debris during cutting and the difficulty in removing these debris efficiently after the machining process. For silicon substrates, this debris can interfere with surrounding components and cause problems during bonding with other substrates by preventing uniform conformal contact. This study delves deep into the challenges faced and methods to overcome them during laser micromachining based manufacturing of such complicated 3D - Manifolded micro-cooler (3DMMC) structures. Specifically, this work summarizes several post-process techniques that can be employed for complete debris removal during etching of Silicon samples using an Nd/YVO4 ultraviolet (UV) laser, detailing the advantages and drawbacks of each approach. A method that was found to be particularly promising to achieve very smooth surfaces with almost complete debris removal was the use of Polydimethylsiloxane (PDMS) as a high rigidity protective coating. In the process, a novel technique to strip PDMS from Silicon surface was also developed. The result of this study is valuable to the micro-fabrication industry where smooth and clean substrate surfaces are highly desirable and it will significantly improve the process of using UV lasers to create microstructures for commercial applications as well as in a research environment.