Remove the turtle and place it in a separate cleaned area / large container.
Allow the turtle and shell to "dry" or gently pat dry the shell with a clean cloth towel.
With a soft toothbrush, GENTLY wipe the affected areas on the shell (but not the neck!).
Thoroughly apply liberal amounts Betadine (found at most drug stores) to the affected areas on the shell.
Swab the infected neck area with Betadine using Q-tips.
Also using a Q-tip, apply Nolvasan or Neosporin ointment (also found at most drug stores) to the affected areas on the shell. You can also add some to the neck area.
Leave the turtle in this area / container for at least an hour or two before returning to the tank (observe and keep an eye on the turtle while it is in the area / container because it may try to climb out and inadvertently hurt itself or flip over.
Repeat the procedure every day
Good luck.