This study presents an automated methodology for evaluating micro-channels fabricated using a femtosecond laser on stainless steel substrates. We utilize 3D surface topography and metrological analyses to extract geometric features and detect fabrication defects. Standardized samples were analyzed using a light interferometer, and the resulting data were processed with Principal Component Analysis (PCA) and RANSAC algorithms to derive channel characteristics, such as depth, wall taper, and surface roughness. The proposed method identifies common defects, including bumps and V-defects, which can compromise the functionality of micro-channels. The effectiveness of the approach is validated by comparisons with commercial solutions. This automated procedure aims to enhance the reliability and precision of femtosecond laser micro-milling for industrial applications. The detected defects, combined with fabrication parameters, could be ingested in an AI-based process to optimize fabrication processes.