To add a rectangle annotation to a PDF Document page.

async function main() {
  const doc = await PDFNet.PDFDoc.createFromURL(filename);
  const page = await doc.getPage(1);

  // Create a rectangle
  const squareAnnot = await PDFNet.SquareAnnot.create(
    doc,
    new PDFNet.Rect(500, 200, 580, 300)
  );
  await squareAnnot.setColor(await PDFNet.ColorPt.init(1, 0, 0), 3);
  await squareAnnot.setInteriorColor(await PDFNet.ColorPt.init(0, 1, 1), 3);
  const dash = [4, 2];
  await squareAnnot.setBorderStyle(
    await PDFNet.AnnotBorderStyle.createWithDashPattern(
      PDFNet.AnnotBorderStyle.Style.e_dashed,
      6,
      0,
      0,
      dash
    )
  );
  await squareAnnot.setPadding(new PDFNet.Rect(4, 4, 4, 4));
  await squareAnnot.refreshAppearance();
  await page.annotPushBack(squareAnnot);
}
PDFNet.runWithCleanup(main);

Add or edit PDF annotations sample
Full code sample which shows how to add or edit PDF annotations (e.g. hyperlink, intra-document link, stamp, rubber stamp, file attachment, sound, text, free-text, line, circle, square, polygon, polyline, rectangle, squiggly, caret, and ink).