Start with the PDF, not the reference library
Highlights are easiest to extract when they are saved as real PDF annotations inside the file. That means the marked text, page location, color, and any attached comment travel with the PDF itself instead of living only inside a reader app database.
Many readers can display highlights before those highlights are embedded in the PDF. Zotero, Mendeley, Preview, and Acrobat store and export annotations differently.
PDF reader
Highlights and comments
Annotated PDF
Annotations embedded
PDF Highlights App
Quotes, notes, page numbers
Use the export path for your reader
Before extracting highlights, make a fresh annotated copy from the app where you did the reading. This preserves the source file and gives the extractor a clean PDF to inspect.
For Zotero, export or save an annotated PDF copy. For Mendeley, use its export-with-annotations option when available. For Preview, save or export the PDF without printing it. For Adobe Acrobat, save the annotated PDF or export comment data when you specifically need FDF or XFDF files.
- Zotero: use Export PDF or Save As from the PDF reader so Zotero annotations are embedded.
- Mendeley: use Export PDF with annotations from the file menu, context menu, or file options where available.
- Preview: use Save, Export, or Export to PDF. Print > Save as PDF can flatten editable annotations.
- Adobe Acrobat: save the PDF after commenting, or use the comments list export tools for FDF/XFDF comment data.
Check the annotated copy before processing
Open the exported PDF in a second reader and confirm that the highlights remain visible and selectable. Missing highlights indicate an export that did not embed them. Unselectable marks were likely flattened into the page image.
Use an annotated PDF with selectable highlights. PDF Highlights App can then retain the highlighted text, comment, color, page number, and source PDF name.
Extract many PDFs into one workspace
Once each source PDF contains its annotations, import the files together. Review quotes by project, group related passages, search across documents, and export notes for writing.
For research and legal work, keep the original PDFs and the exported annotated copies. The original is your untouched source; the annotated copy is the practical working file for highlight extraction.