I have a fillable pdf. In which i have few textboxes.
I fill these fields by using following code(itextsharp).
DataTable dt = new DataTable();
Your code line
stamper.FormFlattening = true;
instructs iTextSharp to flatten the form fields, i.e. to integrate them into the page content and remove the form field annotations.
As you want to keep the form fields as editable fields, don't flatten the form.