In this study, to more quantitatively evaluate the structural characteristics of an ultra-precision machine for machining large-surface micro-features, the joint stiffnesses of hydrostatic guideways and bearings were identified based on a virtual prototype and compliances of the ultra-precision machine. The virtual prototype of the ultra-precision machine was constructed to include the joint stiffnesses to be identified, and the joint stiffnesses were identified through an optimization problem in order to minimize the error between the compliances measured from the physical prototype and the compliances predicted from the virtual prototype. In particular, the validity of the identified joint stiffnesses was verified by the fact that the loop stiffnesses of the ultra-precision machine predicted from the virtual prototype and the identified joint stiffnesses coincided well with those measured from the physical prototype.