To add a highlight annotation to a PDF Document page.

$doc = new PDFDoc($filename);
$page = $doc->GetPage(1);

// Create a highlight
$hl = HighlightAnnot::Create( $doc->GetSDFDoc(), new Rect(100.0,490.0,150.0,515.0) );
$hl->SetColor( new ColorPt(0.0,1.0,0.0), 3 );
$hl->RefreshAppearance();
$page->AnnotPushBack( $hl );

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, highlight, squiggly, caret, and ink).