Coordinate measuring machines are widely used in the industrial field due to their ease of automation. However, estimating the measurement uncertainty is a delicate task, especially when controlling for deviation, given the large number of factors that influence the measurement. A precise estimate of the uncertainty is crucial to avoid incorrect conformity assessments. The purpose of this study is to control geometrical-form tolerance specifications, taking into consideration their associated uncertainty. A surface fitting model based on the least squares criterion is proposed, allowing one to obtain the variance–covariance matrix by iterative calculation according to the Levenberg–Marquard optimization method. The form deviation is then evaluated following the Geometrical Product Specifications (GPS) Standard, and its associated uncertainty is estimated using the guide to the expression of uncertainty in measurement (GUM) propagation of the uncertainty law. Finally, the conformity assessment is performed based on the measured deviation and its associated uncertainty. Different results for the measurement of straightness, flatness, circularity, roundness, and cylindricity are presented and detailed. This model is thereafter validated by a Monte Carlo simulation, and interlaboratory comparisons of the obtained results were performed, which showed satisfactory outcome. This contribution is of great use to manufacturing companies and metrology laboratories, allowing them to meet the normative guidelines, which stipulates that each measurement result must be accompanied by its associated uncertainty.