In addition to reading laid-out documents, the most popular purposes for PDFs are forms and annotation. As far as filling in PDF forms are concerned, I have just one word to say: Fillably, Joel Norvell’s outstanding app available from the App Store, which transforms Preview into the ideal platform for tax and other forms. Rather than struggling with the tangle of tools in a general PDF editor, Fillably provides the perfect suite for creating PDF forms.

Annotating PDFs is more complicated, though.

Encoding annotations

Annotations aren’t an afterthought, but a central part of PDF. All PDF documents consist of a list of hundreds or thousands of objects of different types, including annotations of the Annot type, and those are listed in one of the file’s standard dictionaries, its Annotations Dictionary, Annots.

There are at least 27 sub-types of Annot, including Caret, Highlight and Stamp, which are reflected in the annotation tools provided by apps from Acrobat to Preview. Seemingly complex annotations like popup notes are straightforward to code in PDF, requiring just two linked objects, one for the popup and its text, the other to specify its placement on the page. Others are more involved, as they can extend to include file attachments, sound, movie and other multimedia.

PDF versions

Despite their original simplicity, there are multiple problems that can arise with annotations.

With more recent versions of PDF, the ways in which they can be coded has increased. Mark up a PDF using the latest versions of Adobe Acrobat Reader or its ‘Pro’ CC colleague and they’ll cast it in PDF-1.6 and you’re unlikely to see a single Annot in their source. Most apps built on the Quartz PDF engine should write their files in PDF-1.3 so they can be accessed more widely, and should use regular Annot sub-types throughout. However, Preview likes to use opaque AAPL:AKAnnotationObjects that you won’t encounter anywhere else.

What Quartz does is to ‘flatten’ each PDF into a common 1.3 format for rendering, and that can be saved to disk. At present, that seems to work faithfully, but might give the impression that macOS can’t render more recent versions of PDF, which isn’t true. You can demonstrate that by opening an Acrobat PDF-1.6 document using an app that relies on the Quartz engine, such as PDF Expert, Preview or my Podofyllin, and comparing that with the original in Acrobat.

Podofyllin has a convenient feature for doing just that, in its source window. The uppermost of its three views displays Quartz ‘flattened’ code in PDF-1.3, the middle shows the original, here in PDF-1.6, and the lowermost is a summary of the latter.

Hidden annotations

The biggest dangers with annotations arise because of PDF’s ancient origins and a file format that doesn’t make sufficiently clear distinction between data and metadata. All annotations are metadata added to the underlying document, but in PDF, objects for each are mixed freely within the source. When they’re clearly distinguished with the Annot type, they should be easy to remove as a group, and PDF Expert offers that as a convenient command. That’s ideal when a document has been developed with the aid of reviewers’ annotations, to prepare the finished version for release.

Unfortunately this can cause its own problems, as PDF source is notorious for retaining old content that’s no longer visible in the rendered document, but can be read by anyone with a little knowledge about PDF. Like incomplete redactions, such hidden annotations have caused many embarrassments in the past, and will continue to catch folk out.

Preview’s bugs

Finally, Preview has had more than its fair share of bugs in handling PDF annotations. During my research for this article, Preview 11.0 (1069.7.1) in macOS 15.6 was generally well behaved, but did mangle comments added to a test document by PDF Expert and Adobe Acrobat. Preview has two behaviours that can appear disconcerting: that of its Highlights and Notes tool, and its use of versioning.

All Preview’s tools are single-shot apart from Highlights and Notes, the drawing pencil icon to the left of its popup menu. Click this once to apply highlighting to selected blocks of text, and to remove existing highlighted sections. Unfortunately when this tool is turned on, its own highlighting is so weak that it’s hard to see.

Overwritten files

Preview has a habit of saving PDF documents automatically when closing them, without any warning. If it has just mutilated an annotation, for example, you might assume the original file has just been overwritten and lost. However, Preview saves PDFs using the macOS document versioning system, so you can always recover the previous version.

This might at first seem an impossible task: use Preview to restore that old version and it will repeat its mutilation, defeating the purpose. Yet the original PDF editor won’t have access to previous versions, as it doesn’t use the versioning system. The solution is to use Revisionist, or Versatility, which can save the original as a separate document.

Key points

• Annotations are a central feature of PDF, come in many sub-types, and can be complicated as they can be expressed in different ways.
• The macOS Quartz PDF engine transforms them into PDF-1.3, which makes them simpler and more explicit, so they can be saved ‘flattened’.
• PDF format mixes document data with metadata and annotations.
• Few PDF editors offer to remove all annotations, and there’s a risk of some remaining hidden from view, but still remaining in the PDF source, potentially causing embarrassment when they’re discovered.
• Preview’s earlier bugs in annotations have improved, but it can still mutilate those made by other PDF editors.
• If Preview saves a mutilated PDF, you should be able to recover the previous version of that file using Revisionist or Versatility.