If the fungus is gone but the marks remain, they are most likely etching damage to the lens coating, or possibly the glass itself. In that case, there is nothing left on the surface to clean off.

So the short answer is: no, those marks generally cannot be removed by normal cleaning. Fixing them would require polishing or recoating, which is usually impractical for most lenses.

If the damage is only in the coating, the lens may still be usable, though contrast and flare resistance can be affected. If the glass itself is etched, the damage is permanent.