Laser micromachining can serve as a coarse machining step during sample preparation for high-resolution characterization methods leading to swift sample preparation. However, selecting the right laser parameters is crucial to minimize the heat-affected zone, which can potentially compromise the microstructure of the specimen. This study focuses on evaluating the size of heat-affected zone in laser annular milling, aiming to ascertain a minimal scan diameter that safeguards the inner region of micropillars against thermal damage. A computational model based on the finite element method was utilized to simulate the laser heating process. To validate the simulation results, a picosecond pulsed laser is then used to machine the micropillars of Al and Si. The laser-machined samples were subjected to surface and microstructural analysis using Scanning Electron Microscope (SEM) and Electron Backscatter Diffraction (EBSD) scans. The length of heat affected zone obtained from simulations was approximately 6 μm for silicon and 12 μm for aluminum. The diameter of micropillars formed with laser machining was 10 μm for silicon 26 μm for aluminum. The core of the pillars was preserved with less than one degree of microstructural misorientations making it suitable for further processing for preparing specimens for techniques like APT and TEM. For silicon micropillars, the preserved central region has a diameter of 6 μm and for aluminum its around 20-24 μm. Additionally, the study determines the minimum scan diameter that can be achieved using the given laser machining setup across a range of common materials.