This paper introduces an intelligent and automated system proposed for EDM hole drilling of super-alloys in manufacturing and re-manufacturing stages of products used in aerospace, die/mold and medical surgery. The system is a user-friendly computer-based program, which guides the end-user in order to perform sustainable and effective process. To accomplish the goals of the work, a well-planned workshop tests have been performed via drilling of micro and macro-scale holes (0.4-3 mm) on Ti-6AI-4V and Inconel 718 alloys, which are commonly used in aerospace industry and medical sector for manufacturing of highly critical components. The experimental data was refined and analysed using ANOVA to obtain parameter's relations and mathematical modelling for optimisation. ANFIS has been adopted to correlate the EDM hole drilling parameters (i.e. pulse current, pulse duration/interval, capacitance, material removal rate, electrode wear and surface roughness) for fulfilling reliable, cost/time effective and efficient hole making operations.