using (var file = new FileStream(filename, FileMode.Open, FileAccess.Read))
{
   var document = PdfReader.Open(file);
   document.SecuritySettings.OwnerPassword = "aaaaaaaa";

   var ms = new MemoryStream();
   document.Save(ms, false);
   ms.Flush();
   ms.Position = 0;

   using (FileStream output = new FileStream(outputFile, FileMode.Create, FileAccess.Write))
   {
      StreamUtility.CopyStream(ms, output, 32768);
   }
}