Array of arrays is probably the best data structure. The trick in using it is to pull elements off the front of each nested array to get the output data as you need it:

#use strict;
use warnings;

my $File1 = <<FILE;
13
34
32
20
43
FILE

my $File2 = <<FILE;
22
15
27
33
48
65
34
FILE

my $File3 = <<FILE;
18
20
22
45
44
32
12
26
FILE

my @data;

for my $file (\$File1, \$File2, \$File3) {
    open my $fIn, '<', $file or die "Can't open $file: $!\n";
    
    push @data, [];
    
    while (<$fIn>) {
        chomp;
        push @{$data[-1]}, $_;
    }
}

while (grep {@$_} @data) {
    printf "%s\n", join "\t", map {$_ // ''} map {shift @$_} @data;
}
[download]

Prints:

13    22    18
34    15    20
32    27    22
20    33    45
43    48    44
    65    32
    34    12
        26
[download]

Thanks a lot Grandfather, the trick of printing was what I needed. As for you 2teez, I really don't understand your attitude. I explicitly said where I am stuck, so I needed help with that. You didn't want to help, fair enough, but please don't judge people you don't know.

Where is the judgement? I don't see it. I simply refer you to a link that boldly stated among other things that ..Be precise about the correct behavior / desired output. Additional background about what you are trying to do and what you have tried also helps.

If I don't want to help, I would not even put in a word to start with.
I don't think "I want to .." like your OP says shows what you have tired and I don't think asking to shows some what of what you have tired a crime.
We all came here either to help or to be helped, and then make the world a better place!

Till you come out of the shadows, enjoy yourself friend!

If you tell me, I'll forget.
If you show me, I'll remember.
if you involve me, I'll understand.
--- Author unknown to me

The oneliner has a BEGIN block to copy @ARGV to the first row of the @AoA then use the current line number $. to choose wich column fill with the current $_ while the current starting column is governed by the $x which is increased every new file read (when eof is reached ARGV is also closed to reset $. ) The END block dump the @aoa in the desired format.

I've changed your sample files (for my sanity) so that file1.txt only contains numbers starting with 1 and so on.

perl -lnE "BEGIN{$aoa[0]=[@ARGV]}$aoa[$.][$x]=$_; if(eof){close ARGV;$
+x++}END{map{say join ',',@$_}@aoa}" file1.txt file2.txt file3.txt

file1.txt,file2.txt,file3.txt
13,22,38
14,25,30
12,27,32
10,23,35
13,28,34
,25,32
,24,32
,,36
[download]

L*

Any tips?

Use paste.

Yeah, its called paste/csvpaste.pl or a pivot table

$ paste file1 file2 file2
File1   File2   File2
13      22      22
34      15      15
32      27      27
20      33      33
43      48      48
        65      65
        34      34
[download]