The quality of micro-features in various technologies is mostly affected by the choice of the micro-fabrication technique, which in turn results in several limitations with regard to materials, productivity, and cost. Laser beam micro-machining has a distinct edge over other non-traditional methods in terms of material choices, precision, shape complexity, and surface integrity. This study investigates the effect of laser fluence and pulse overlap while developing microchannels in alumina ceramic using an neodymium-doped yttrium aluminum garnet (Nd:YAG) laser. Microchannels 200 µm wide with different depths were machined using different laser peak fluence and pulse overlap (percentage of overlap between successive laser pulses) values. It was found that high pulse overlaps and fluences should be avoided as they give rise to V-shaped microchannels i.e., 100% bottom width errors. The optimal peak fluence range was found to be around 125–130 J/cm2 corresponding to 3–5 µm depth per scan. In addition, channels fabricated with moderate pulse overlap were found to be of good quality compared to low pulse overlaps.