CodeEval Challenge: Remove specified characters from a string
You can extract out the requirement into its own method:

private static String removeCharacters(String input, String excludedLetters) {
    // ...
}


And since you have to split from a single String first, you can use a wrapper method in addition to the one above:

private static String removeCharacters(String line) {
    String[] parts = // ...
    return removeCharacters(parts[0], parts[1]);
}


If you are on Java 8, you can use a combination of try-with-resources and Files.lines() to Streamline the processing (pun intended):

try (Stream&lt;String&gt; lines = Files.lines(Paths.get(/* ... */))) {
    lines.map(Main::removeCharacters).forEach(System.out::println);
}