I'd use Imager::Fill.

#!/usr/bin/perl

use strict;
use warnings;
use Imager;
use Imager::Fill;

my $fill = Imager::Fill->new(type => "opacity",
           other   => $fill,
           opacity => 0.25);
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where $fill is The Imager::Fill object you want to modify, and the default opacity is 0.5. You can modify the opacity to get the level of tranparency that you want.