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

    // Remove shape by reference
    doc.Pages[0].Shapes.Remove(doc.Pages[0].Shapes[0]);

    doc.Save();
}