UPDATE: Please see https://softwarerecs.stackexchange.com/questions/71464/java-library-to-insert-invisible-text-into-a-pdf instead.
I want to insert invisible text i
3 options. My answers are itext-specific, but you should be able to translate the underlying methods to any sufficiently advance PDF library.
myPdfContentByte.setTextRenderMode(PdfContentByte.TEXT_RENDER_MODE_INVISIBLE);
myPdfStamper.getUnderContent(pageNum)
makes this easy, and will let you draw the text under the scan. Other libraries that let you access a page's contents might require you to add your text 'in the raw' at the beginning of an existing content stream. You'll want to check out the "PDF Spec" (google that, you'll be fine) for details. Chapter 9 is all about text rendering.