Actually, as I read it, you want to be able to read in a PDF with multiple pages and from each page in turn, generate an image of that page with a barcode overlaying part of the image, then take that page image and write it as a .png file.
You can use iText to read the PDF, but that's about its limit. If the pages in the PDF have more than just raw images in them - for example, they have typeset text - then you would need a way to interpret those typesetting commands and overlay the text onto the image workspace. You would also have to use a barcode font/generator library to overlay the barcode into the image space. Finally you'd use
Java's image writer functions to output the image space as a PNG-format (NOT PDF!!!) file. Ensuring it has been given a ".png" file extension is just part of the standard file output.