Я нашел это!
LayerUtility lu = new LayerUtility( doc );
PDXObjectForm form = lu.importPageAsForm( doc2, 0 );
PDPage page = (PDPage) doc.getDocumentCatalog().getAllPages().get( 0 );
lu.wrapInSaveRestore( page );
AffineTransform at = new AffineTransform();
lu.appendFormAsLayer( page, form, at, "new_layer_name" );