Drilling of micro-holes for micro-electrical-mechanical systems and its applications are critical. In present work, micro-holes are drilled on a low melting point material, perspex. Microwave energy is used to drill holes through thermal ablation at 2.45 GHz. The drilled holes are analysed under field emission scanning electron microscope (FESEM) based on backscattering. The experimental results show a fine drilled hole with minimum heat affected zone (HAZ) and no delamination. Asmooth curve with an average diameter of 846 micron was successfully drilled on a 5mm thick perspex sample. Surface integrity around the hole was studied by atomic force microscope (AFM) through Ra, Rp, Rz, Rv, Rt, Rku and Rq values. AFMis used to generate values at three variants as near to hole, at average HAZ and at the end of HAZ boundary. Energy dispersive spectroscopy (EDS) is used to study the material degradation in terms of changes in composition at five different zones. The Vickers hardness tester at Hv 0.05 was used to understand the hardness variation at three regions of HAZ. The XRD analysis was used to confirm the formation of the crystalline surface around the amorphous hole. The customised process is developed in-house to study the performance of microwave power, drill time, ablation, residue and (HAZ). The results confirm enhanced drilling of the hole at low power (90W) by a steel alloy concentrator, which otherwise worsens with an increase of power beyond 180W without significant variation in HAZ beyond 360 W.