The milling of thermally modified wood is a very broad topic that deserves attention. The acquired knowledge concerning the geometry of the tool and milling process may assist manufacturers in designing new tools and thus improving the efficiency and quality of the process. This article focuses on finding the differences in the roughness of wood surfaces after surface milling of native beech wood (Fagus sylvatica L.) and thermally modified beech wood at 190 °C and differing technological conditions, cutting speeds (20, 30, and 40 m/s), feed speeds (4, 8, and 11 m/min), and rake angles of the tool (15°, 20°, and 25°). In comparison with natural wood, thermal treatment had a positive effect on the quality of the wood surface after milling. The results also demonstrated an increased quality of surface finish with a decrease in feed speed and increase in cutting speed.