The anisotropic behavior of the material microstructure when processing multiphase materials at microscale becomes an important factor that has to be considered throughout the machining process. This is especially the case when chip-loads and machined features are comparable in size to the cutting edge radius of the tool, and also similar in scale to the grain sizes of the phases present within the material microstructure. Therefore, there is a real need for reliable models, which can be used to simulate the surface generation process during microendmilling of multiphase materials.This paper presents a model to simulate the surface generation process during microendmilling of multiphase materials. The proposed model considers the effects of the following factors: the geometry of the cutting tool, the feed rate, and the workpiece material microstructure. Especially, variations of the minimum chip thickness at phase boundaries are considered by feeding maps of the material microstructure into the model. Thus, the model takes into account these variations that alter the machining mechanism from a proper cutting to ploughing and vice versa, and are the main cause of microburr formation. By applying the proposed model, it is possible to estimate more accurately the resulting roughness because the microburr formation dominates the surface generation process during microendmilling of multiphase materials. The proposed model was experimentally validated by machining two different samples of dual-phase steel under a range of chip-loads. The roughness of the resulting surfaces was measured and compared to the predictions of the proposed model under the same cutting conditions. The results show that the proposed model accurately predicts the roughness of the machined surfaces by taking into account the effects of material multiphase microstructure. Also, the developed model successfully elucidates the mechanism of microburr formation at the phase boundaries, and quantitatively describes its contributions to the resulting surface roughness after microendmilling.