In order to guarantee the quality of a freeform curve and to get more meaningful analysis results, it is essential to be aware of all uncertainties resources and their impact on the estimation. In this work, a more sophisticated uncertainty budget is considered, that contributes to a refined covariance matrix. Uncertainties are modelled and propagated according to the “Guide to the Expression of Uncertainty in Measurements (GUM)”. Furthermore, control points of B-Spline curves are estimated by means of the least-squares methods based on the refined VCM. Comparison have been made between the B-Spline curves using identity and refined weight matrix, which reflects that the uncertainty influence within the estimation cannot be neglected for high quality results.