In milling operations, tangential and normal cutting forces induce normal, tangential and axial elastic tool deformations. Tool mounting in the machine spindle may also contribute to kinematical errors. There is reason to believe that this phenomenon affects the milled surface formation and 3D surface topology parameters of final surface. We performed simple, flat-end milling operations on C45 steel to compare results of surface total height measurements and prediction results done by using mathematical model developed by this article authors. Surface measurements were taken with an optical 3D surface topography evaluating device. Analysis identified significant tool deflections during the high-speed milling process. These combined with kinematical inaccuracies produce a complex tool movement that is basically responsible for the surface topology formation and 3D surface roughness parameter values. A similar approach could also be used to analyse more complex milling operations, such as those used in die and mould manufacturing.