In micro-manufacturing, the accurate prediction of defects affecting the part quality by means of process simulations is of paramount importance. With this purpose, micro-injection moulding process simulations can be fundamental with the aim of strongly reducing experimental and quality assurance efforts. In this study, the usage of process simulations for the prediction of the size of the flash affecting an ultra-small three-dimensional polyoxymethylene (POM) micro component is discussed. A three-dimensional multi-scale mesh was used to discretize a geometry comprising the part and the feed system of the one-cavity micro mould. The venting channel was included into the model in order to simulate the flash formation as a virtual short-shot. Simulation were run with Autodesk Moldflow Insight 2017® and results validated by comparing numerical results with experimental observation of the flash size. A state-of-the-art 3D focus variation measurement instrument was used for characterizing the flash on moulded parts. Four injection moulding process parameters were tested using a Design of Experiment (DoE) approach in both real experiments and simulations in order to validate the numerical outputs with respect to process variations. The results showed that flash size was generally overestimated by simulations. However, both real parts measurements and numerical results agreed on the signs and magnitudes of the effects of the investigated process parameters, demonstrating that simulations are an useful tool for process/product optimization.