I am assuming the marks are not machining or sanding marks left on the tube, anodize will not hide machining marks. Native oxide can be difficult to remove chemically, sanding or beadblasting is the most effective way.
If the tube was formed by DOM (drawn over mandrel) but not then annealed, there will be work hardening present on the surface. These work hardened areas will anodize differently then those areas not work hardened. The solution to this is annealing the tube, to bring the entire tube to the same level of hardness. You may also be able to machine or sand the entire outside surface of the tube to remove the offending hardened areas.
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