my @filelist = ('zip1.zip','zip2.zip','zip3.zip');

##</code><code>##

zip1.zip
-->file1.txt
-->file2.txt

zip2.zip
-->directory1 (dir)
---->file1.txt
---->file3.txt
-->file4.txt

zip3.zp
-->file5.txt
-->file6.txt
-->file7.txt

##</code><code>##

bigzip.zip
-->zip1 (dir)
---->file1.txt
---->file2.txt
-->zip2 (dir)
---->directory1 (dir)
------>file1.txt
------>file3.txt
---->file4.txt
-->zip3 (dir)
---->file5.txt
---->file6.txt
---->file7.txt

##</code><code>##

my $zip = Archive::Zip->new();
foreach (@filelist) {
    my $file = Archive::Zip->new($_});

    foreach ($file->members()){
        $zip->addMember( $_ );
    }
}

##</code><code>##

bigzip.zip
-->file1.txt
-->file2.txt
-->directory1 (dir)
---->file1.txt
---->file3.txt
-->file4.txt
-->file5.txt
-->file6.txt
-->file7.txt

##</code><code>##

my $x=1;
my $zip = Archive::Zip->new();
foreach (@filelist) {
    my $file = Archive::Zip->new($_);
    my $directoryname = 'zip'.$x;

    foreach ($file->members()){
        my $m = $zip->addMember( $_ );
        $m->fileName($directoryname.'/'.$m->fileName());
    }

    $x++;
}