The study deals with the micro holes surface morphology, surface roughness and micro cracks of AISI 316 machined by EDM drilling process and examined by atomic force microscope (AFM) technique. Experiments were conducted by considering the process parameters of current, pulse-on time, and pulse-off time with a copper electrode of 300 μm diameter. The experiments were planned according to Taguchi L9 orthogonal array. The outcomes of experiments are surface texture and surface roughness after the machining process shown excellent with low pulse energy parameters. The average surface roughness Ra was 5–20 nm for the 300 μm diameter microholes, over the scanning area. Additionally, the AFM application generated information about the 3D surface imaging, recast layer, and micro-cracks on micro hole of AISI 316 stainless steel. These findings highlight the effectiveness of AFM as a superior tool for evaluating the surface characteristics of micro holes in AISI 316 stainless steel, offering potential advancements in precision EDM drilling machining applications.