How to NOT "Print" a section by using Print module?
In those cases I added a custom print--pdf.tpl.php file to my theme and defined my custom css in the head of the HTML page which is rendered in this file (you find the original template file named "print.tpl.php" in the print modules folder - just copy it to your theme and rename it).

Here you can define any element by CSS and give it a "display: none;" - so it will not be seen in your final PDF.