The effectiveness and precision of electric discharge machining (EDM) in fabricating holes in challenging materials rely on the careful choice of suitable tools, materials, and process parameters. Nevertheless, the productivity and material removal rate (MRR) of the EDM process impacted by unstable machining conditions and inadequate removal of debris, especially when drilling holes with high aspect ratios. This study focused on examining how various machining conditions influenced the response variables TWR, MRR, and hole taper (HT) were investigated for with different thickness of plates, namely 0.5 mm(W1), 1 mm (W2), and 1.5 mm (W3) of Ti-6Al-4V. The Taguchi based L9 orthogonal array used to design the experiment and the obtained results were subjected to analysis using Analysis of Variance (ANOVA). The effective implementation of appropriate flushing techniques, efficient debris evacuation, and consistent maintenance of machining conditions resulted in enhanced performance for rotary micro EDM (µ-EDM). However, the µ-EDM process is influenced by numerous operating parameters. The findings revealed that the percentage contribution of capacitance and electrode rotation speed (ERS) is more significant compared to voltage. Specifically, for the W3 workpiece, capacitance displayed utmost MRR 0.01894 mm3/min, which is 51.12% and 63.10% greater than the W1 and W2 workpieces respectively. In contrast, the W1 workpiece exhibited the least TWR of 0.000193 mm3/min, which was 50.61% and 67.24% lower than the W2 and W3 workpieces respectively. The W1 workpiece enhanced accuracy as it significantly reduced the HT as compared to the W2 and W3 workpieces. Scanning Electron Microscopy (SEM) was utilized to investigate how workpiece thickness and process parameters influence the surface quality of micro-holes during manufacturing. Through SEM analysis, present study examined the effects of voltage, capacitance, ERS and thickness of the workpiece on the micro-hole surfaces, enabling a deeper understanding of their impact on the final product's quality.