#!/usr/bin/perl
use warnings;
use strict;

my $file1 = reader('file1.txt');
my $file2 = reader('file2.txt');

foreach my $col ( 0 .. $#{$file1} ) {
    print @{ $file1->[$col] }, @{ $file2->[$col] }, $/;
}

sub reader {
    my ($file) = @_;
    my @array;
    open my $fh, '<', $file or die "can't open file:$!";
    while ( defined( my $line = <$fh> ) ) {
        chomp $line;
        next if $line =~ m/^$/;
        push @array, [ split /\s+/, $line ];
    }
    close $fh or die "can't close file:$!";

    return \@array;
}