The research presents methodologies to identify and simulate manufacturing defects in three-dimension, and simple indicators for evaluating the global quality of a fixture. We then developed a model for simulating positioning defects of a workpiece that is fixed on a three-jaw chuck. This model is a combination of three methods: design of experiments, finite element simulation, and Monte Carlo simulation. Three factors, which are assumed to be the most important in positioning defects, are used in this model. Based on the simulated results, the influences of these factors are estimated. The results obtained from simulations can be expressed by form of distributions or statistical parameters. These allow using simulation of tolerance analysis based on Monte Carlo simulation. Finally, a model is developed based on MMP for tolerance analysis. This model allows us to verify a given process plan with functional tolerances of the machined part by determination of a number of machined parts out of tolerance zones or determine functional tolerances of a batch of machined parts based on a given process plan (without functional tolerances) and a number of rejected parts per million.