I read each line as a string then converted the whole thing to a 2D array. This isn't the full code, but the technique works for me

    Scanner in =  new Scanner(System.in);
    int n = in.nextInt();
    char [][]charArray = new char[n][n];

    for (int i = 0; i < n; i++)
    {
        String lines = in.next();
        charArray[i] = lines.toCharArray();
    }

    for (int i = 1; i < n-1; i++)
    {
        for(int j = 1; j < n-1; j++)
        {
            if((charArray[i][j] > charArray[i-1][j]) && (charArray[i][j] > charArray[i+1][j]) && (charArray[i][j] > charArray[i][j-1]) && (charArray[i][j] > charArray[i][j+1]))
                charArray[i][j] = 'X';
        } 
    }