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// For complete examples and data files, please go to https://github.com/groupdocs-watermark/GroupDocs.Watermark-for-.NET
using (PdfDocument doc = Document.Load<PdfDocument>(Utilities.MapSourceFilePath (FilePath)))
{
    // Remove Annotation by index
    doc.Pages[0].Annotations.RemoveAt(0);

    // Remove Annotation by reference
    doc.Pages[0].Annotations.Remove(doc.Pages[0].Annotations[0]);

    doc.Save();
}