Are endnotes easier to extract than footnotes?

Yes, generally. Endnotes sit together in one contiguous block at the end of a chapter or document, so extracting them is largely a matter of grabbing that section and splitting it into numbered entries — clean and predictable. Footnotes are scattered at the bottom of each page, interleaved on the page with body text and separated from it only by position and size (not by any structural tag), so pulling them cleanly requires distinguishing the page-bottom note region from the main text on every page. So if a work uses endnotes, count yourself lucky; if it uses footnotes, expect more layout-based work and a verification pass. Either way the PDF has no built-in "this is a note" marker, so extraction is inference.

How do I reconnect notes to their reference markers?

The superscript markers in the body (¹, ², or [1], [2]) and the notes themselves are separate pieces of text, so to rebuild the linkage you extract both — the markers with their positions in the body, and the notes with their numbers — and pair them by number. For endnotes this is straightforward (note 12 pairs with marker 12). For footnotes you also have to be sure you matched the right page's notes. If you only need the note content (the citations or commentary), you can skip the markers entirely. Decide up front whether you need the linkage or just the notes; the linkage is more work and only worth it if you actually use it.

How do I build a consolidated notes document?

Once extracted, you often want all the notes (and/or references) gathered into one clean document — a consolidated list you can read, search, or process further. Pull the notes from each page or the endnote block, put them in order, and assemble them into a single document (convert to an editable format if you will edit them). For reference-style notes, this consolidated list is effectively your bibliography from the work. Keeping the notes as real, searchable text (not an image) means you can search across them, which is much of the value for research. A consolidated, ordered, searchable notes document is usually the goal.

Can I turn the notes into citations?

Where notes contain bibliographic references (common in humanities footnotes, and in any reference list), yes — extract the references and, where each has a DOI or enough detail, regenerate proper citations for your reference manager rather than retyping. The most reliable path is to recover each reference's DOI and rebuild the citation from an authoritative source in your needed style. For discursive notes (commentary rather than references), there is nothing to "cite" — you just keep the text. So separate the two: reference-bearing notes become citations; commentary notes stay as text. The reference list at the end is usually the cleanest source of citations.

What if the PDF is scanned?

OCR it first — a scan is images with no text. Notes are a hard OCR case: the small note font is recognised less accurately than body text, superscript markers and dense reference abbreviations are easily misread, and a wrong character in a citation is a real error. So OCR, then extract, then verify carefully against the original, especially page numbers, years, and author names. For a scanned scholarly work where you need accurate citations, budget real verification time rather than trusting the OCR. The order is fixed: OCR → extract notes → reconnect/consolidate → verify.

How do I verify the extraction is complete?

Check counts and separation. Count the note markers in the body against the number of extracted notes — they should match, and a mismatch means a note was missed or two were merged. Confirm notes were cleanly separated from body text (no body sentences captured as notes, no notes left inline). For endnotes, check the block was fully captured (first to last number). Spot-check a sample of references against the original. Because note extraction is inference-based, "extract then verify" is essential — the automated result is a strong draft, not guaranteed-correct, especially on footnote-heavy or scanned works.

Is it safe to process an unpublished paper online?

Unpublished or under-review papers are confidential, so prefer a tool that processes files locally. ScoutMyTool extracts text, OCRs, and formats citations entirely in your browser tab, so the paper never leaves your machine. For anything pre-publication, confirm the tool does not upload before using it.

5 min read

How to extract footnotes and endnotes from academic PDFs

By ScoutMyTool Editorial Team · Last updated: 2026-05-22

Footnotes and endnotes carry a scholarly work’s citations and commentary, and getting them out of a PDF cleanly depends a lot on which kind you are dealing with: endnotes sit together at the end and come out easily, while footnotes are scattered page by page and interleaved with the body, making them the harder case. This guide covers extracting both — why endnotes are easier, how to reconnect notes to their markers when you need the linkage, how to build a consolidated, searchable notes (or citations) document, handling scans, and verifying completeness. It is the companion to our footnote-focused guide, here covering endnotes and the full notes workflow.

Note kinds and extraction difficulty

Note kind	Location	Difficulty
Footnotes	Bottom of each page	Harder — interleaved with body per page
Endnotes	End of chapter/document	Easier — one contiguous block
Reference list	End, structured	Easiest — parse by entry
Mixed (notes + refs)	Both	Extract separately, then combine

Step by step — extract notes cleanly

Identify footnotes vs. endnotes. Endnotes → grab the end block; footnotes → work page by page. This decides your approach.
OCR scans first. Recover text with PDF OCR (see OCR + reformat) and verify the small note text.
Extract the notes. For footnotes, separate the page-bottom region per page — the technique in extracting footnotes; for endnotes, split the contiguous block by number.
Reconnect to markers if needed. Pair body markers to notes by number; skip if you only need note content.
Consolidate into one document. Order the notes and assemble them (convert to editable with PDF to Word if editing) into a searchable notes list.
Turn references into citations. For reference-bearing notes, build citations with the Citation Formatter — see citation export.
Verify completeness. Count markers vs. notes, check separation, and spot-check references against the original.

Extract footnotes: the footnote-focused companion.
Paper management & citation export: turning references into citations.
Academic research workflow: managing scholarly documents.
OCR + reformat: for scanned works.
PDF to spreadsheet: structured reference extraction.
Citation Formatter: build citations from references.
All ScoutMyTool PDF tools: the full toolkit.

FAQ

Are endnotes easier to extract than footnotes?: Yes, generally. Endnotes sit together in one contiguous block at the end of a chapter or document, so extracting them is largely a matter of grabbing that section and splitting it into numbered entries — clean and predictable. Footnotes are scattered at the bottom of each page, interleaved on the page with body text and separated from it only by position and size (not by any structural tag), so pulling them cleanly requires distinguishing the page-bottom note region from the main text on every page. So if a work uses endnotes, count yourself lucky; if it uses footnotes, expect more layout-based work and a verification pass. Either way the PDF has no built-in "this is a note" marker, so extraction is inference.
How do I reconnect notes to their reference markers?: The superscript markers in the body (¹, ², or [1], [2]) and the notes themselves are separate pieces of text, so to rebuild the linkage you extract both — the markers with their positions in the body, and the notes with their numbers — and pair them by number. For endnotes this is straightforward (note 12 pairs with marker 12). For footnotes you also have to be sure you matched the right page's notes. If you only need the note content (the citations or commentary), you can skip the markers entirely. Decide up front whether you need the linkage or just the notes; the linkage is more work and only worth it if you actually use it.
How do I build a consolidated notes document?: Once extracted, you often want all the notes (and/or references) gathered into one clean document — a consolidated list you can read, search, or process further. Pull the notes from each page or the endnote block, put them in order, and assemble them into a single document (convert to an editable format if you will edit them). For reference-style notes, this consolidated list is effectively your bibliography from the work. Keeping the notes as real, searchable text (not an image) means you can search across them, which is much of the value for research. A consolidated, ordered, searchable notes document is usually the goal.
Can I turn the notes into citations?: Where notes contain bibliographic references (common in humanities footnotes, and in any reference list), yes — extract the references and, where each has a DOI or enough detail, regenerate proper citations for your reference manager rather than retyping. The most reliable path is to recover each reference's DOI and rebuild the citation from an authoritative source in your needed style. For discursive notes (commentary rather than references), there is nothing to "cite" — you just keep the text. So separate the two: reference-bearing notes become citations; commentary notes stay as text. The reference list at the end is usually the cleanest source of citations.
What if the PDF is scanned?: OCR it first — a scan is images with no text. Notes are a hard OCR case: the small note font is recognised less accurately than body text, superscript markers and dense reference abbreviations are easily misread, and a wrong character in a citation is a real error. So OCR, then extract, then verify carefully against the original, especially page numbers, years, and author names. For a scanned scholarly work where you need accurate citations, budget real verification time rather than trusting the OCR. The order is fixed: OCR → extract notes → reconnect/consolidate → verify.
How do I verify the extraction is complete?: Check counts and separation. Count the note markers in the body against the number of extracted notes — they should match, and a mismatch means a note was missed or two were merged. Confirm notes were cleanly separated from body text (no body sentences captured as notes, no notes left inline). For endnotes, check the block was fully captured (first to last number). Spot-check a sample of references against the original. Because note extraction is inference-based, "extract then verify" is essential — the automated result is a strong draft, not guaranteed-correct, especially on footnote-heavy or scanned works.
Is it safe to process an unpublished paper online?: Unpublished or under-review papers are confidential, so prefer a tool that processes files locally. ScoutMyTool extracts text, OCRs, and formats citations entirely in your browser tab, so the paper never leaves your machine. For anything pre-publication, confirm the tool does not upload before using it.

Citations

Wikipedia — “Note (typography),” on footnotes and endnotes. en.wikipedia.org/wiki/Note_(typography)
Wikipedia — “Citation,” on the references notes often carry. en.wikipedia.org/wiki/Citation
Wikipedia — “PDF” (ISO 32000), the position-based model with no native note concept. en.wikipedia.org/wiki/PDF

All the notes, gathered and searchable

Extract footnotes and endnotes, OCR scans, and turn references into citations with ScoutMyTool’s in-browser tools — your papers never leave your machine.

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