At first your should set up a printer service
PrintService printService = PrintServiceLookup.lookupDefaultPrintService();
and then use a print presenter for the comparison
new PDFComparer()
.addPresenter( new DifferencesPrintPresenter( printService, new HashPrintRequestAttributeSet()) )
.compare( <file1>, <file2> );
This setting will use the default printer, if any. To define the printer to be used, the attribute set has to be filled.