bookmarking and OCR documents

Report · Jul 19, 2022

I have a document that I've bookmarked, but I also need to convert it to OCR in Adobe. How do I do this? when I upload the bookmarked document to a filing service, that service automatically converts the document to text searchable and removes the bookmarking.

Report · Jul 19, 2022

Hi Geneen

Hope you are doing well and sorry to hear that.

Adobe Acrobat DC supports both OCR and Bookmarks. Go to Tools> Enhance Scan> Recognize Text

What happens when you try to run the OCR on the PDF file? Do you get any error message? If yes, please share the screenshot of the same for a better understanding.

What is the filing service you are uploading the PDF document to? Please try uploading a different PDF file and see if its an issue with a specific file or not.

Also, make sure you have the recent version 22.1.20169 installed for Acrobat DC. Go to help > Check for updates and reboot the computer once.

We are here for help, just need more information.

Regards

Amal

Report · Jul 19, 2022

It would be better to get the document filing service not to throw away the bookmarks...

ABAMBO | Hard- and Software Engineer | Photographer

Report · May 06, 2025

To convert a bookmarked PDF to OCR in Adobe Acrobat while preserving bookmarks and addressing the issue of a filing service removing bookmarks, follow these steps. This guide assumes you’re using Adobe Acrobat Pro, as OCR functionality is limited in Acrobat Reader.

Step 1: Verify the Document Needs OCR

Check if the PDF is already searchable: Open the PDF in Adobe Acrobat. Try to select or highlight text. If you can’t, it’s likely a scanned or image-only PDF requiring OCR.
Confirm bookmarks exist: Open the Bookmarks panel (View > Show/Hide > Navigation Panes > Bookmarks or press Ctrl+B). Ensure your bookmarks are visible and correctly linked to their respective pages.

Step 2: Apply OCR in Adobe Acrobat Pro

Adobe Acrobat Pro’s OCR feature converts scanned or image-based text into searchable, editable text while generally preserving existing bookmarks.

Open the PDF: Launch Adobe Acrobat Pro and open your bookmarked PDF.
Access the OCR tool:

Go to Tools > Scan & OCR (in versions after October 2023, this is under All Tools).
Alternatively, if you open a scanned PDF in edit mode, Acrobat may automatically prompt to run OCR.

Run OCR:

In the Scan & OCR panel, select In This File under Recognize Text.
Choose the appropriate language for text recognition (e.g., English) to improve accuracy.
Select Recognize Text. Acrobat will process the document, making the text searchable and selectable.

Optional: Enhance the scan:

If the scan quality is poor, use the Enhance File options in the Scan & OCR tool to clean up the image (e.g., deskew or adjust contrast). Note that this doesn’t automatically recognize text; you’ll still need to run Recognize Text afterward.

Correct recognized text (if needed):

In the Scan & OCR tool, select Correct Recognized Text. Check the Review recognized text box, review any suspect text, correct errors, and click Accept.

Save the file:

Go to File > Save As, choose a location, and save the PDF. This ensures the OCR data and bookmarks are embedded in the file.

Step 3: Verify Bookmarks Post-OCR

Reopen the Bookmarks panel (Ctrl+B) to confirm that bookmarks are intact and still link to the correct pages. Adobe Acrobat’s OCR process typically preserves bookmarks, as they are stored as metadata separate from the text layer.
If bookmarks are missing or misaligned, you may need to recreate them:

Go to the desired page, select text or an area, and choose Tools > Edit PDF > More > Add Bookmark. Edit the bookmark label as needed.
Alternatively, if the document has a structured table of contents, use Bookmarks > New Bookmarks From Structure to regenerate bookmarks (if the document is tagged).

Step 4: Address Filing Service Removing Bookmarks

Some filing services (e.g., court eFiling systems) automatically process uploaded PDFs, which can strip bookmarks or other metadata. To mitigate this:

Test the OCR’d PDF:

Before uploading, confirm the PDF is text-searchable (try searching for a word using Ctrl+F) and bookmarks are intact.

Check filing service requirements:

Review the service’s documentation for PDF specifications (e.g., PDF/A compliance, restrictions on metadata, or automatic OCR processing). For example, some court systems like Florida’s Second District Court of Appeal require bookmarks for documents with indexes.
If the service applies its own OCR, it may overwrite or ignore existing OCR layers and strip bookmarks, as you’ve observed.

Workarounds to preserve bookmarks:

Flatten the PDF: Before uploading, flatten the PDF to embed bookmarks and OCR data into a single layer. In Acrobat Pro:

Go to File > Print, select Adobe PDF as the printer, and choose Flatten Annotations and Form Fields in the print settings. Save the new PDF. This may reduce the likelihood of the filing service altering the file. (Note: Flattening is not explicitly detailed in the provided sources but is a common Acrobat technique.)

Export bookmarks to a text file: If bookmarks are consistently removed, export them for reference or reapplication:

Use a tool like JPDFBookmarks (free, requires Java) to export bookmarks to a text file before uploading. After the filing service processes the PDF, reimport the bookmarks into the processed file.
Alternatively, in Acrobat Pro, export the PDF as HTML with bookmarks as a navigation frame, copy the bookmark text, and manually recreate them if needed.

Contact the filing service: Ask if they can disable automatic OCR or metadata stripping for your uploads. Provide a PDF that’s already text-searchable to bypass their processing. Some services allow pre-OCR’d PDFs to retain original metadata

Step 4: Save and Upload

Save a backup: Keep a copy of the original and OCR’d PDF with bookmarks before uploading to the filing service.
Upload and verify: Upload the OCR’d PDF to the filing service. After processing, download the filed version and check if bookmarks are preserved. If not, use the exported bookmark text to recreate them or adjust your workflow based on the service’s limitations.

Troubleshooting Tips

OCR fails or text is inaccurate: Ensure the scan is high quality (300 DPI or higher) and select the correct language in OCR settings. Use Enhance File options for poor scans.
Bookmarks disappear in Acrobat: If bookmarks are lost during OCR, the PDF may have security settings restricting edits. Check File > Properties > Security and ensure bookmark modifications are allowed.
Filing service issues persist: If the service continues to strip bookmarks, test uploading a PDF/A-compliant file (convert using File > Save As > PDF/A in Acrobat) or consult the service’s support for specific PDF requirements.

Notes

Adobe Acrobat Pro is required for full OCR functionality; the free Acrobat Reader lacks advanced OCR tools.
If cost is a concern, PDFelement or free tools like PDF-XChange Editor may suffice for OCR and bookmarking.
For complex documents, consider adding tags post-OCR (in Tags Pane, right-click No Tags Available > Add Tags to Document) to improve accessibility and bookmark stability.

If you encounter specific errors during this process or need guidance on a particular filing service, please provide more details, and I can tailor the solution further.