Can I replace groups in Java regex?

Use $n (where n is a digit) to refer to captured subsequences in replaceFirst(...). I'm assuming you wanted to replace the first group with the literal string "number" and the second group with the value of the first group.

Pattern p = Pattern.compile("(\\d)(.*)(\\d)");
String input = "6 example input 4";
Matcher m = p.matcher(input);
if (m.find()) {
    // replace first number with "number" and second number with the first
    String output = m.replaceFirst("number $3$1");  // number 46
}

Consider (\D+) for the second group instead of (.*). * is a greedy matcher, and will at first consume the last digit. The matcher will then have to backtrack when it realizes the final (\d) has nothing to match, before it can match to the final digit.

You could use Matcher#start(group) and Matcher#end(group) to build a generic replacement method:

public static String replaceGroup(String regex, String source, int groupToReplace, String replacement) {
    return replaceGroup(regex, source, groupToReplace, 1, replacement);
}

public static String replaceGroup(String regex, String source, int groupToReplace, int groupOccurrence, String replacement) {
    Matcher m = Pattern.compile(regex).matcher(source);
    for (int i = 0; i < groupOccurrence; i++)
        if (!m.find()) return source; // pattern not met, may also throw an exception here
    return new StringBuilder(source).replace(m.start(groupToReplace), m.end(groupToReplace), replacement).toString();
}

public static void main(String[] args) {
    // replace with "%" what was matched by group 1 
    // input: aaa123ccc
    // output: %123ccc
    System.out.println(replaceGroup("([a-z]+)([0-9]+)([a-z]+)", "aaa123ccc", 1, "%"));

    // replace with "!!!" what was matched the 4th time by the group 2
    // input: a1b2c3d4e5
    // output: a1b2c3d!!!e5
    System.out.println(replaceGroup("([a-z])(\\d)", "a1b2c3d4e5", 2, 4, "!!!"));
}

Check online demo here.