Visible scratches aren't a big deal as long as everything else is done right.
If you really want to get rid of them, spend a lot more time at the 4K level, or get a stone in the neighborhood of 2k. Even then, you will still probably have some visible scratches. What's interesting is when you look under a microscope, as you go up in grits and especially with stropping - they become softer with a rounded profile even though they are still visible. IME visible scratches don't affect the shave quality.