Microstructure diagnostics and failure analyses are pivotal for the ongoing improvement of functional materials and sophisticated components. Using ultra-short pulses and optimized processing routes laser processing is entering the scene of sample preparation, speeding up processes and opening up access to deeply buried structures and large-area preparation. In the present paper, novel approaches for sample preparation using ultra-short pulsed laser micromachining are introduced and their practical application is demonstrated via illustrative examples in the field of nano-X-ray computer tomography (nano-CT), transmission electron microscopy (TEM) and atom-probe-tomography (APT). Furthermore, concepts for sample cleaning within the laser micromachining tool, as well as results addressing the laser affected zone arising in different materials which have been analyzed using TEM and Raman spectroscopy will be presented.