The laser micro-drilling of “thru” holes, also known as via holes, in Si, InP and InSb semiconductor wafers was studied using millisecond pulse lengths from an IPG Laser Model YLR-2000 CW multimode 2 kW Ytterbium Fibre Laser and a JK400 (400 W) fibre laser, both with 1070 nm wavelength. The flexibility of this laser wavelength and simple pulsing scheme were demonstrated for semiconductor substrates of narrow (InSb Eg 0.17 eV) and wide (InP Eg 1.35 eV)) room-temperature bandgap, Eg, with respect to the photon energy of 1.1 eV. Optical microscopy and cross-sectional analysis were used to quantify hole dimensions and the distribution of recast material for all wafers and, for silicon, any microcracking for both (100) and (111) single crystal surface Si wafer orientations. It was found that the thermal diffusivity was not a sufficient parameter for predicting the relative hole sizes for the Si, InP and InSb single crystal semiconductors studied. Detailed observations for Si showed that, between the threshold energies for surface melting and the irradiance for drilling a “thru” hole from the front surface to rear surface, there was a range of irradiances for which micro-cracking occurred near the hole circumference. The directionality and lengths of these microcracks were studied for the (100) and (111) orientations and possible mechanisms for formation were discussed, including the Griffith criterion for microcracks and the failure mechanism of fatigue usually applied to welding of metals. For Si, above the irradiance for formation of a thru-hole, few cracks were observed. Future work will compare similar observations and measurements in other narrow- and wide-bandgap semiconductor wafer substrates. We demonstrated one application of this laser micro-drilling process for the micro-fabrication of a thru hole precisely-located in the centre of a silicon-based atom chip which had been patterned using semiconductor lithographic techniques. The end-user application was a source of magneto-optically trapped (MOT) cold atoms of Rubidium (87Rb) for portable quantum sensing.