In this study, to minimize trial and error in the design and manufacturing processes of a high-precision large-surface micro-grooving machine which is able to fabricate the molds for 42 inch LCD light guide panels, the effects of the structural deformation of the micro-grooving machine according to the positions of the X-axis, Y-axis and Z-axis feed systems were examined on the tool tip displacement errors associated with the machining accuracy. The virtual prototype (finite element model) of the micro-grooving machine was constructed to include the joint stiffnesses of the hydrostatic bearings, hydrostatic guideways and linear motors, and then the tool tip displacement errors were measured from the virtual prototype. Especially, to establish the prediction model of the tool tip displacement errors, which was constructed using the positions of the X-axis, Y-axis and Z-axis feed systems as independent variables, the response surface method based on the central composite design was introduced. The reliability of the prediction model was verified by the fact that the tool tip displacement errors obtained from the prediction model coincided well those measured from the virtual prototype. And the causes of the tool tip displacement errors were identified through the analysis of interactions between the positions of the X-axis, Y-axis and Z-axis feed systems.