#!/usr/bin/perl

use warnings;
use strict;
use List::Util qw/max/;

my $VAR1 = {
  'sample.txt' => [
    'Line_1_3long',
    'Line_2_3'
  ],
  'sample_2.txt' => [
    'Line_3_3longer'
  ],
  'sample_3.txt' => [
    'Line_4_3',
    'Line_5_3',
    'Line_6_3evenlonger',
    'Line_7_3',
  ]
};

my %maxlength = ();
foreach my $key (sort keys %$VAR1) {
  $maxlength{$key} = max map { length } @{$VAR1->{$key}};
}

my $maxelements = max map { $#$_ } values %$VAR1;

foreach my $line (0..$maxelements) {
  foreach my $key (sort keys %$VAR1) {
    if($line >= @{$VAR1->{$key}}) {
      print " " x ($maxlength{$key} + 1);
    } else {
      print $VAR1->{$key}->[$line];
      print " " x ($maxlength{$key} - length($VAR1->{$key}->[$line]) + 1);
    }
  }
  print "\n";
}

##</code><code>##

$ perl test.pl
Line_1_3long Line_3_3longer Line_4_3
Line_2_3                    Line_5_3
                            Line_6_3evenlonger
                            Line_7_3
$