High-speed milling has often been applied in injection mold manufacturing processes, where surface roughness is a significant criterion in product quality demands. It is equally applicable to automotive or industrial engineering and to toy manufacturing, where plastic parts with a high-quality surface finish have been processed using the injection molding technique. High-speed milling involves a number of process parameters that may affect the 3D surface topography formation. Literature analysis reveals that dynamical behavior is a significant factor in the end milling process on surface roughness parameters. To improve the accuracy of predicted surface topography models, it is important to include the dynamical behavior of milling factor. This paper describes the surface prediction model of combined end-milling geometrical and dynamical interaction models. The natural frequency of machine assembly and forced vibrations during the cutting process were measured during the flat-end milling process. Unevenly distributed cutting marks were revealed by surface 3D topography images and microscopy images of the machined samples. A mathematical model to predict surface topography was developed, including dynamical behavior and cutting geometries. Machine accuracy also has to be addressed. 3D surface topography parameters from the experimental sample provided the results for the mathematical prediction model. This model offers a software tool for manufacturers to improve the quality of machined part surfaces, taking into account the behavioral properties of their machining equipment. Relevant conclusions about the manufacturing equipment accuracy have been drawn. Vibrations in the milling system affect the cutting process and contribute to the surface topography prediction model. Local cutting tool vibrations do not have any influence on surface parameter mean values.