Here is a sample Java program showing how to remove all link annotations present in a PDF document using Qoppa’s PDF library jPDFProcess:

// Load PDF document
PDFDocument pdfDoc = new PDFDocument ("C:\\myfolder\\input.pdf", null);
int pageCount = pdfDoc.getPageCount();
// loop through pages
for (int i = 0; i < pageCount; i++)
{
  try
  {
    PDFPage page = pdfDoc.getPage(i);
    Vector annots = page.getAnnotations();
    // loop through annotations
    for (int j = 0; j < annots.size(); j++)
    {
     Annotation annot = (Annotation) annots.get(j);
     // if link then remove it
     if (annot instanceof Link)
     {
        page.removeAnnotation(annot);
        count++;
      }
    }
  }
  catch (PDFException e)
  {
  e.printStackTrace();
  }
}
System.out.println("Number of links removed " + count);