Aluminum anodizing is typically in the order of 5 to 100 micrometers thick, depending on the process. Anodizing will build up vertically on the surface and won’t “fill in” the machining marks. So under the right lighting, the scratches will always be visible. However, there are a vast number of post-processing finishes that can reduce or even eliminate these marks altogether to give a completely smooth finish for anodizing.

Before spending money on expensive post-processing I would tell the machinist that your intent is to anodize and that machining marks must be limited as much as possible. Machining marks can be almost completely eliminated depending on the complexity of the part or the skill of the machinist. A word of warning though, improved surface finishes will result in a more expensive part so only request better finishes on areas that will be visible.