In recent years, research to machine large-surface micro-features has become important because of the light guide panel of a large-scale liquid crystal display and the bipolar plate of a high-capacity proton exchange membrane fuel cell. In this study, in order to realize the systematic design technology and performance improvements of an ultra-precision machine for machining the large-surface micro-features, a structural characteristic analysis was performed using its virtual prototype. The prototype consisted of gantry-type frame, hydrostatic feed mechanisms, linear motors, brushless DC servo motor, counterbalance mechanism, and so on. The loop stiffness was estimated from the relative displacement between the tool post and C-axis table, which was caused by a cutting force. Especially, the causes of structural stiffness deterioration were identified through the structural deformation analysis of sub-models.