We present a new approach for precision prediction of parallel kinematics machine tools by virtual prototyping (VP) using advanced software tools. VP modelling and kinematics simulation using MSC/ADAMS was carried out for the proposed parallel drilling module mounted on a serial milling machine base, to perform a 3-PRS-PP hybrid-mechanism-based machine tool. The related kinematic analysis, such as the displacement and velocity analysis of the drilling tool end, the rotation angle analysis of the ball joints, the linear movements of the prismatic joints, is obtained. Kinematics analyses and simulations were carried out with and without manufacturing and assembly deviations. The effects of deviations on machine performances were analysed using two-dimensional probability distribution analysis. We present the application of a virtual prototype simulation approach in the parametric design process, structural design and error budget determination for new types of machine tools.