PDF Editing Issues

How to Remove Highlights and Underlines from a Flattened PDF

Steven Parker Oct 19, 2026 868 views

Question details

The user needs to erase annotations such as highlights, underlines, and strikethroughs that have been flattened and permanently merged into a PDF document's base content.

How to Remove Highlights, Underlines, and Strikethroughs from a Flattened PDF

Product: PDF
Device & OS: not provided
Scenario: Attempting to clean up or edit a PDF document where previous annotations were flattened during the printing or exporting process.
Observed behavior: The highlights and underlines act as embedded graphical elements within the PDF page. Standard annotation tools cannot select, edit, or delete them, and applying new highlight colors simply overlaps, leaving the original color or a visible halo.

Before you start

Check your computer or cloud storage to see if you still have access to the original source document (such as a Word or PowerPoint file), as editing the source is the most reliable way to fix flattened annotations.

Solution 1Recommended

Remove Annotations from the Original Source Document

The most effective method is to modify the source file before converting it to a PDF again, entirely bypassing the flattened PDF constraints.

When a document is printed to PDF, separate layers like annotations are compressed into a single, flat image. Because the PDF no longer recognizes the highlights as editable text features, fixing the original file is highly recommended.

Open the source file

Locate and open the original document (e.g., Microsoft Word, Google Docs) from which the flattened PDF was originally created.

Clear the formatting

Highlight the affected text blocks and use your word processor's text formatting tools to select 'No Color' for highlights or remove underlines and strikethroughs.

Re-export to PDF

Go to 'File', select 'Save As' or 'Export', and choose the PDF format. Ensure you export the document natively rather than using a 'Print to PDF' function that forces flattening.

Remove Annotations from the Original Source Document

Best Practice: This method ensures 100% preservation of your document's layout and text quality without relying on complex PDF editing tools.

Solution 2

Convert the Flattened PDF to a Word Document

If you do not have the source file, converting the PDF back into an editable Word document can help isolate and delete the embedded markings.

Easily Convert and Edit Flattened PDFs with WPS Office

WPS Office provides a powerful, all-in-one PDF toolkit that includes an accurate PDF to Word converter. This feature allows you to extract text from flattened PDFs, easily delete embedded highlight backgrounds in WPS Writer, and recreate a perfectly clean document.

1. Open your PDF in WPS: Launch WPS Office and open your flattened PDF document from the home screen.
2. Convert to Word: Navigate to the 'Tools' tab on the top ribbon and click on 'PDF to Word' to begin the conversion process.
3. Edit the document: Once the conversion finishes, the file will automatically open in WPS Writer. Select the unwanted background colors or highlight shapes and delete them.
4. Export the clean file: Click 'Menu' in the top-left corner, select 'Export to PDF', and save your freshly cleaned document.

Highly accurate PDF to Word conversion to salvage flattened documentsBuilt-in PDF editing tools for managing standard annotations and textFull compatibility with Microsoft Office formats (Docx, Xlsx, Pptx)Free, lightweight, and features an intuitive tabbed interface

microsoft office alternative - wps office

Frequently Asked Questions

Why can't I click or delete the highlight in my PDF?

When a PDF is 'flattened', interactive elements like highlights, strikethroughs, and form fields are permanently merged into the visual background layer of the page. Because of this, standard PDF selection tools no longer recognize them as separate, editable objects.

Does highlighting over a flattened highlight change its color?

No. Standard PDF highlighters use a multiply blending mode. Highlighting over an existing flattened color will simply mix the two colors together, often resulting in a darker shade or leaving a visible halo around the text instead of cleanly replacing it.

Can I just cover the flattened highlight with a white box?

Yes, as a workaround, you can use the 'Add Shape' or drawing tools in your PDF editor to place a solid white rectangle with no border over the flattened highlight. You can then add a transparent text box over the white shape to retype the text. However, this method is highly time-consuming for large documents.

PDF Troubleshooting