A reviewed document comes back wearing a layer that is not part of the page at all: sticky notes with their pop-up windows, a wash of highlights, somebody's freehand circles, an “Approved” stamp, the boxes of a half-filled form. All of that sits in each page's annotation list, and it comes off by kind rather than all at once — comments and highlights gone, links kept, form fields untouched until you say otherwise. The pieces are joined up, so the tidying is the interesting part: a note's pop-up and its replies leave with the note, a field that loses its last box leaves the form's field tree, and a tagged document's structure tree stops pointing at things that no longer exist. Nothing is painted over; the marks are gone, not covered.
Features
Seven kinds to pick from: comments, highlights, drawings, stamps, links, form fields and everything else
A count per kind and per individual annotation type before anything is touched
Every page, or a list such as 2, 5-9
A note's pop-up window and any replies to it leave with the note
Fields that lose their last box leave the form, and an XFA description goes with them
Nothing is drawn over the page — a removed mark disappears rather than being hidden
Warnings for choices that change behaviour, such as breaking a clickable contents list
A tagged PDF's structure tree is tidied so it no longer points at what has gone
How to use the Remove PDF Annotations
Drop the PDF in and see what sits on it, counted by kind
Choose every page, or list the pages to clean
Tick the kinds to remove — links and form fields start unticked
Remove, check the preview, and save the clean copy
Removed 55 annotations: 12 comments & notes, 40 highlights & text markup, 3 stamps. The link stayed.
The pop-up windows belonging to those notes went too, and were never counted twice.
Common errors & troubleshooting
A highlight is still there after removing everything. — It was flattened into the page by whoever produced the file, so it is part of the printed artwork rather than a mark lying on top of it. Only redaction or a fresh copy of the original can take that out.
The form can no longer be filled in. — Form fields were among the kinds removed, which deletes the boxes and whatever had been typed into them. To keep the answers and stop further editing, flatten the form instead.
The clickable contents list stopped working. — Links were ticked. Untick Links and run it again; the contents entries are link annotations like any other.
Redaction marks vanished but the text under them is still readable. — Those marks had never been applied. A redaction mark is only a proposal until it is carried out, so removing it hides nothing — use PDF Redactor to actually take the content out.
Frequently asked questions
Why does a highlight sometimes survive being removed?
Because it is no longer an annotation. Flattening bakes marks into the page's own drawing instructions, at which point they are as much part of the page as the text. This tool works on the annotation layer, and a flattened mark has left it.
What happens to the pop-up window of a sticky note?
It leaves with its note, wherever on the page it was parked, along with any replies in the comment thread. It is also never counted as a comment of its own, so the numbers match what a reader shows you.
Can I strip the comments but keep the links?
Yes, and that is the default. Links and form fields start unticked precisely because removing them changes how a document works rather than just how it looks.
Does removing a form field delete what was typed into it?
Yes. The value lives in the field, so both go together and the form can no longer be completed. When the answers matter, flatten the form: the text stays visible on the page and nobody can edit it.
Could a removed comment be recovered from the saved copy?
The saved document is rewritten without those objects and without the references that reached them, so there is nothing left to recover from it. The original file on your disk is untouched, as always.
Related tools
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PDF Privacy Scanner — Find the metadata and personal data hiding inside a PDF.
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PDF Sanitizer — Remove JavaScript, auto-run actions, embedded files and other active content from a PDF.
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PDF Metadata Editor — View, edit or strip a PDF’s title, author, subject, keywords and producer.
Extract Links from PDF — Collect every clickable link and written URL in a PDF, with page numbers, as CSV.
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Organize PDF — Reorder, rotate and delete pages from thumbnails, then export.
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PDF to Text — Extract selectable text from a PDF as plain text or Markdown.
Compare PDFs — Diff the extracted text of two PDFs line-by-line.
Encrypt PDF — Password-protect a PDF with AES-256 or RC4 encryption.
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Compress PDF — Shrink a PDF by re-rendering each page to a JPEG at a chosen quality and resolution.
PDF Metadata Editor — View, edit or strip a PDF’s title, author, subject, keywords and producer.
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Flatten PDF — Lock filled form fields into the page so a PDF looks the same everywhere.
PDF N-up — Print 2, 4, 9 or 16 pages per sheet, with a booklet option for folding.
Interleave PDF Pages — Merge odd and even scan passes back into one document, reversing if needed.
PDF to Single Long Page — Stack every page onto one continuous sheet you scroll instead of paging.
PDF Form Data Extractor — Pull the answers out of a filled PDF form as JSON or CSV, field by field.
Blank Page Remover — Find and delete blank pages from a scan, with a tolerance you control.
Text to PDF — Turn typed or pasted text into a paginated, downloadable PDF.
Markdown to PDF — Render Markdown — headings, lists, tables and code — as a PDF.