In addition to their attractive mechanical properties, the lack of grain boundaries and crystal defects of Bulk Metallic Glasses (BMGs) make them suitable materials for integration in micro-systems fabrication chains, either as final components or mould inserts. The application of short or ultra-short pulsed lasers has recently been demonstrated for the processing of BMGs in this context, particularly as a possible solution for machining micro-scale features on the surface of BMG workpieces. Therefore, complementary studies that consider both experimental and thermal simulation data at the same time in the context of multiple and moving pulses irradiating a BMG specimen are desirable to gain insight into micromachining phenomena. Although such models have been reported in the context of single pulse processing of BMG substrates, their extension to multiple pulse scenarios for micromachining is lacking. Thus, the overall objective of this paper is to combine both theoretical and experimental laser micromachining investigations using multiple pulses when irradiating a BMG workpiece. The specific focus is on conducting such laser operations in the nanosecond regime on a Zr-based BMG, with composition Zr52.5Cu17.9Ni14.6Al10Ti5, also known as Vitreloy 105. This combined experimental and theoretical approach enabled the identification of a suitable set of laser parameters with respect to the process efficiency over a range of pulse duration, fluence values, scanning speed and track distance between machined grooves. In addition, it was highlighted that laser micro-machining operations can lead to BMG materials experiencing thermal cycles, which are quite different from that taking place during the conventional synthesis of glassy alloys, thus complicating the further characterisation and understanding of crystallisation phenomena at play.