An annotation is not part of the page. Understanding that one fact explains every strange thing annotations do.
What an annotation actually is
When you highlight a line, nothing about that line changes. A rectangle object is added to the page's annotation list, positioned over those coordinates, with a colour and a transparency.
The same is true of comments, sticky notes, drawn shapes, stamps and typed text boxes. They sit in a layer above the content, which is why you can drag them, delete them, change their colour, and list them all in a sidebar.
It is also why a highlight can be slightly misaligned. It was placed at coordinates, not attached to words, so if the underlying text renders at all differently the highlight does not follow.
What each tool is for
| Annotation | Best for | Note |
|---|---|---|
| Highlight | Marking text you will return to | Needs a text layer; will not work on a scan |
| Sticky note | A comment that should not clutter the page | Collapses to an icon |
| Text box | Something that must be visible when printed | Sticky notes often do not print |
| Strikethrough | Proposing a deletion | Conventional in review |
| Drawing / freehand | Circling a diagram, signing | Works on scans, since it needs no text |
| Stamp | Status marking — Approved, Draft | Visual only, carries no authority |
The printing row catches people out. Sticky notes are collapsed icons by default and most readers omit them when printing, so a reviewer's carefully written comments arrive on paper as nothing at all. If comments must survive printing, use text boxes, or print the annotation summary separately.
Highlighting a scan
You cannot highlight text on a scanned page, because there is no text to select — the page is a photograph. The highlighter tool simply will not engage.
What works instead is the rectangle or freehand tool with a transparent fill, drawn manually over the area. It looks nearly identical and behaves the same for review purposes.
If you need real text highlighting on a scan, the document needs a text layer first, which means OCR — covered in searchable vs scanned PDFs. Whether that is worth doing depends on whether anyone will search the document later.
Removing them all at once
Deleting annotations one at a time on a forty-page reviewed document is nobody's idea of an afternoon. Every serious reader has a bulk route.
Look for the comments or annotations panel — a sidebar listing every annotation in the file. From there you can select all and delete in one action, which is far faster than hunting them on the pages. Acrobat has it under the Comment tool; Preview lists them in the sidebar; most other readers have an equivalent.
If your reader has no bulk delete, the reliable fallback is to render the pages to images and rebuild — that discards every annotation along with everything else that is not pixels. It also destroys the text layer, so it is a last resort rather than a shortcut.
Flattening: the one-way door
Flattening merges annotations into the page content. The highlight stops being a highlight object and becomes part of the picture of the page.
This is what you want when sending a final document: nobody can drag your signature off, delete a stamp, or edit the comments. It is also irreversible — once flattened, there is no annotation to remove.
- Flatten before sending anything where the annotations are the point: a signed contract, an approved drawing, a marked-up proof.
- Do not flatten a document still in review. The next reviewer needs to be able to respond to and clear the existing comments.
- Keep an unflattened copy. Always. It is the only version you can still change.
- Flattening is not compression. It removes interactive structures, so the file shrinks slightly, but that is a side effect — see why is my PDF so big.
Annotations are not redaction
This is the one that has embarrassed law firms and government departments repeatedly, and it follows directly from what an annotation is.
Drawing a filled black rectangle over sensitive text adds a shape on top. The text underneath is untouched — selectable, copyable, and revealed entirely by deleting the rectangle. The same applies to a black highlight, and to anything described as markup.
True redaction removes the underlying content. If your tool does not say it removes rather than covers, assume it covers. The reliable manual method is in is it safe to share your bank statements — render to images, black out the pixels, rebuild.
Frequently asked questions
Why can I not highlight text in my PDF?
Because it is a scan — there is no text layer to select, so the highlighter will not engage. Use the rectangle or freehand tool with a transparent fill instead, which looks nearly identical. Real text highlighting needs OCR first.
Why do my comments not appear when printed?
Sticky notes are collapsed icons and most readers omit them from print by default. If comments must survive printing, use text boxes instead, or print the annotation summary as a separate document.
How do I delete all highlights at once?
Use the comments or annotations panel — a sidebar listing every annotation in the file — then select all and delete. Hunting them page by page is unnecessary in any serious reader. Acrobat has it under the Comment tool; Preview lists them in the sidebar.
What does flattening a PDF do?
It merges annotations into the page content permanently, so a highlight stops being an object and becomes part of the page image. Do it before sending anything final, so signatures and stamps cannot be dragged off. Keep an unflattened copy — it is irreversible.
Is a black box over text the same as redaction?
No, and this is a genuinely serious mistake. The rectangle is a shape on top; the text underneath is fully selectable and copyable, and deleting the box reveals it. It has caused real disclosure incidents. True redaction removes the content.
Why did my annotations disappear in another reader?
Annotations are stored separately from the page, and support varies — some readers ignore types they do not implement, particularly on mobile and in browser viewers. If they must be visible everywhere, flatten the document before sending.