use PDF::API2;

my $pdf = PDF::API2->open('my.pdf');
my $page = $pdf->openpage(1);
my $gfx = $page->gfx;
my $rect = $gfx->rect(390, 501, 300, 200);
$rect->fillcolor('red');
$rect->fill;

$pdf->saveas("pdfs/myNew.pdf");

# or update:
# $pdf->update();