In answer to my comment, I assume you are using iTextSharp, even though you do not specify. Using iTextSharp, I believe you need to Flatten the form when you are done. Here is a simple example:
public void GeneratePDF(string filePath, List<PDFField> modifiedFields)
{
var pdfReader = new PdfReader(filePath);
var folderStructure = filePath.Split('\\');
if (folderStructure.Length == 0) return;
var currentFileName = folderStructure.Last();
var newFilePath = string.Format("{0}{1}", Constants.SaveFormsPath,
currentFileName.Replace(".pdf", DateTime.Now.ToString("MMddyyhhmmss") + ".pdf"));
var pdfStamper = new PdfStamper(pdfReader, new FileStream(newFilePath, FileMode.Create));
foreach (var field in modifiedFields.Where(f=>f.Value != null))
{
pdfStamper.AcroFields.SetField(field.Name, field.Value);
}
pdfStamper.FormFlattening = true;
pdfStamper.Close();
}
Ignoring the parts about the filename, it boils down to passing in some key value list regarding the field values to set. This could be where you do your signature piece, and then setting the FormFlattening property on the stamper to true.
Here is another SO post where they used a similiar technique for a slightly different issue, it may be of help: How to flatten already filled out PDF form using iTextSharp