I'm using ITextSharp which is forked from IText (a java implemenation fpr pdf editing).
http://sourceforge.net/projects/itextsharp/
http://itextpdf.com/
Edit - this is what you need to do (untested but shoul be close):
using System;
using System.IO;
using iTextSharp.text;
using iTextSharp.text.pdf;
// return processed stream (a new MemoryStream)
public Stream copyAnnotations(Stream sourcePdfStream, Stream destinationPdfStream)
{
// Create new document (IText)
Document outdoc = new Document(PageSize.A4);
// Seek to Stream start and create Reader for input PDF
m.Seek(0, SeekOrigin.Begin);
PdfReader inputPdfReader = new PdfReader(sourcePdfStream);
// Seek to Stream start and create Reader for destination PDF
m.Seek(0, SeekOrigin.Begin);
PdfReader destinationPdfReader = new PdfReader(destinationPdfStream);
// Create a PdfWriter from for new a pdf destination stream
// You should write into a new stream here!
Stream processedPdf = new MemoryStream();
PdfWriter pdfw = PdfWriter.GetInstance(outdoc, processedPdf);
// do not close stream if we've read everything
pdfw.CloseStream = false;
// Open document
outdoc.Open();
// get number of pages
int numPagesIn = inputPdfReader.NumberOfPages;
int numPagesOut = destinationPdfReader.NumberOfPages;
int max = numPagesIn;
// Process max number of pages
if (max<numPagesOut)
{
throw new Exception("Impossible - different number of pages");
}
int i = 0;
// Process Pdf pages
while (i < max)
{
// Import pages from corresponding reader
PdfImportedPage pageIn = writer.inputPdfReader(reader, i);
PdfImportedPage pageOut = writer.destinationPdfReader(reader, i);
// Get named destinations (annotations
List<Annotations> toBeAdded = ParseInAndOutAndGetAnnotations(pageIn, pageOut);
// add your annotations
foreach (Annotation anno in toBeAdded) pageOut.Add(anno);
// Add processed page to output PDFWriter
outdoc.Add(pageOut);
}
// PDF creation finished
outdoc.Close();
// your new destination stream is processedPdf
return processedPdf;
}
The implementation of ParseInAndOutAndGetAnnotations(pageIn, pageOut) needs to reflect your annotations.
Here is a good example with annotations: http://www.java2s.com/Open-Source/Java-Document/PDF/pdf-itext/com/lowagie/text/pdf/internal/PdfAnnotationsImp.java.htm