Micro manufacturing is important for new product applications. As such, due to its size, micro tolerance verification is a challenging task. Optical metrology instruments provide solutions for this task due to their flexibility in accessing the part surface. In addition, it can capture big data in shorter time compared to the tactile (contact) instruments as well as eliminating the risk of damaging the part surface. A fundamental aspect in geometric measurement is traceability, which strictly relates to measurement uncertainty. Only by quantifying uncertainty, measurement results are reliable and comparable each other. Moreover, uncertainty estimation in geometric metrology is not easy since it is “taskspecific” with respect to what is currently measured. In this paper, the importance of measurement uncertainty and its available estimation methods are briefly presented. The implementation of a simulation method to estimate the task specific measurement uncertainty is presented and discussed with a case study.