I'm not sure what you mean when you say you're "not able to" zip your desired directories. In the documentation for Archive::Zip, there is a description of tree operations. The example they give is:

use Archive::Zip;
my $zip = Archive::Zip->new();
# add all readable files and directories below . as xyz/*
$zip->addTree( '.', 'xyz' );  
# add all readable plain files below /abc as def/*
$zip->addTree( '/abc', 'def', sub { -f && -r } );     
# add all .c files below /tmp as stuff/*
$zip->addTreeMatching( '/tmp', 'stuff', '\.c$' );
# add all .o files below /tmp as stuff/* if they aren't writable
$zip->addTreeMatching( '/tmp', 'stuff', '\.o$', sub { ! -w } );
# add all .so files below /tmp that are smaller than 200 bytes as stuf
+f/*
$zip->addTreeMatching( '/tmp', 'stuff', '\.o$', sub { -s < 200 } );
# and write them into a file
$zip->writeToFileNamed('xxx.zip');
# now extract the same files into /tmpx
$zip->extractTree( 'stuff', '/tmpx' );
[download]

This should help you to get started. Note that this module uses the Unix format for path names (forward slashes), even in Windows.

Here's a useful example of how to zip a Windows directory and all subdirectories and gif files, while keeping the original directory structure:

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

use Archive::Zip qw/ :ERROR_CODES :CONSTANTS/;

my $maindir = 'C:\StuffToZip';
my $zipfile = 'backup.zip';

my $zip = Archive::Zip->new();

opendir(MAINDIR, $maindir) or die "Can't open $maindir: $!";
my @folders = readdir(MAINDIR);
foreach (@folders) {
    next if $_ =~ /^\./;
    if (-d "$maindir\\$_") {
        &zip("$_", "$maindir\\$_");
    }
    else {
        print "Error reading $maindir\\$_\n";
    }
}

$zip->writeToFileNamed($zipfile) == AZ_OK or die "Can't write >$zipfil
+e<: $!\n";

closedir MAINDIR;

sub zip {
    my $type        = shift;
    my $dir         = shift;
      #Adds all subdirectories under $maindir and any gif files found
        $zip->addTreeMatching( "$dir", "$type", '\.gif$' );
}
[download]

Hope it helps. Cheers