How to Highlight Scanned PDF and Add Margin Notes

By PDF Agile Team · June 5, 2026 · PDF Annotation Scanned PDF OCR

How to highlight scanned PDF text and add margin notes offline using PDF Agile annotation tool

If you've ever tried to highlight text in a scanned PDF and watched the cursor glide over the page like it's made of glass, you already know the frustration. Scanned PDFs are essentially pictures — every page is a flat image, not a searchable document. That means your standard highlight tool finds nothing to grab onto.

The fix is a two-step process: first run OCR (Optical Character Recognition) to convert the image layer into real, selectable text, then use your annotation tools as normal. This guide walks you through the entire workflow inside PDF Agile — a free offline desktop app — so you never need to upload sensitive documents to the cloud.

By the end you'll be able to highlight scanned PDF pages, add sticky margin notes, and export a clean annotated copy, all without touching the internet.

Scanned PDF vs. Text PDF: Why It Matters

Before diving into steps, it helps to understand what you're working with. The table below shows the key differences:

Scanned PDF vs. Text-Based PDF — Feature Comparison
Feature	Scanned PDF (image)	Text-Based PDF
Text selectable	❌ No	✅ Yes
Searchable	❌ No	✅ Yes
Highlight tool works	❌ Not directly	✅ Yes
Copy/paste text	❌ No	✅ Yes
File size	Larger (image data)	Smaller
Requires OCR first?	✅ Yes	❌ No
Works offline?	✅ After OCR	✅ Always

If your PDF was created by scanning a physical document, photographing pages, or exporting from certain hardware, it's almost certainly image-based. Run OCR and it becomes fully functional.

Step 1 — Run OCR to Make Text Selectable

OCR converts each page image into a hidden text layer that sits behind the visual. Once this layer exists, every annotation tool — highlight, underline, strikethrough, sticky note — works exactly as it does on any normal PDF.

Open your scanned PDF in PDF Agile. Drag the file onto the app window or use Ctrl+O. The page will display normally but you won't be able to select any text yet.

Go to the Tools menu and click OCR. The OCR panel will slide open on the right side of the screen.

Select your document language. Choosing the correct language (e.g., English, Chinese, Japanese) dramatically improves accuracy — especially for documents with mixed scripts or numeric tables.

Choose page range. You can OCR all pages, a custom range (e.g., pages 3–10), or only the current page. For large documents, processing only the pages you need saves time.

Click "Recognize". PDF Agile will process the pages locally on your machine — no internet connection required. A progress bar shows completion. When it finishes, click anywhere on the text: your cursor should now be able to select individual words.

💡 Tip: If text selection still doesn't work after OCR, the original scan may be very low resolution (below 150 DPI). Try printing the document to a PDF printer first to re-rasterize it at a higher DPI, then run OCR again.

Step 2 — Highlight PDF Pages and Passages

With the text layer in place, highlighting works just like in any word processor. Here's the full workflow:

Switch to the Comment tab in the top toolbar. This reveals all annotation tools: Highlight, Underline, Strikethrough, Squiggly, and more.

Click the Highlight tool (yellow marker icon). Your cursor changes to a crosshair/text-select hybrid.

Click and drag over the text you want to mark. Release the mouse — the selected text is immediately highlighted in yellow.

Change highlight color by right-clicking any existing highlight and choosing "Properties". You can switch to green, blue, pink, or any custom color to color-code different themes or topics.

Highlight multiple non-contiguous passages by holding Ctrl while dragging to create additional selections without deselecting previous ones.

Save with Ctrl+S. All highlights are embedded in the PDF file itself — they'll be visible on any PDF reader that supports standard annotations (Adobe Reader, Foxit, Preview on Mac, etc.).

Step 3 — Add Margin Notes to PDF

Margin notes let you attach contextual commentary without altering the original document body. PDF Agile supports two main types: sticky notes (floating callout bubbles) and text boxes (inline positioned text).

Add Sticky Notes to PDF

Select the Sticky Note tool from the Comment tab (looks like a small square speech bubble). This is the standard free pdf reading markup tool used across most PDF editors.

Click anywhere on the page margin — or directly on the text you're commenting on. A small icon will appear at that point and a text input box will open.

Type your note into the popup. You can include questions, summaries, follow-up reminders, or cross-references. Click outside the box to collapse it — the icon remains on the page.

Hover over the icon at any time to preview the note without opening it. Double-click to edit.

💡 Tip: Right-click a sticky note icon → "Properties" to change the icon style (Note, Comment, Key, Help, Insert, Paragraph) and color. Different colors help you distinguish between question notes, summary notes, and action-item notes at a glance.

Add Text Box Annotations in the Margin

Select the Text Box tool from the Comment tab. Unlike sticky notes, text boxes display their content directly on the page — ideal for margin annotations that should always be visible.

Click and drag in the margin area to draw a text box of the size you need.

Type your annotation. Use the format toolbar to adjust font size, weight, and color so the margin note visually contrasts with the document body.

Troubleshooting: Highlight Tool Grayed Out or Not Working

⚠️ Common Issue: The highlight tool appears grayed out or selections don't stick after OCR. Here are the most likely causes and fixes.

Document is password-protected: The PDF owner may have restricted annotations. Go to File → Properties → Security to check. You'll need the owner password to unlock editing permissions.
OCR didn't complete successfully: Check that the OCR process finished without errors. Low-DPI scans (under 150 DPI) can cause partial recognition. Try re-scanning at 300 DPI if possible.
Wrong tool selected: Make sure you're on the Comment tab, not the Edit tab. The Edit tab's text tools are for editing document content, not adding annotations.
Flattened or certified PDF: Some PDFs are "flattened" — all annotations are merged into the page image and no further annotations are allowed. In this case, print to PDF first to create a fresh, unrestricted copy.

Alternative Tools for Highlighting Scanned PDFs

PDF Agile works great for offline, privacy-first workflows. But here are a few alternatives worth knowing:

🔵

Adobe Acrobat Pro Paid

Industry standard. Excellent OCR accuracy across 40+ languages. Expensive subscription model (~$24/month). Best for enterprise workflows requiring certified signatures alongside annotations.

🟣

UPDF Freemium

Modern UI with solid OCR and annotation tools. Free tier adds a watermark on export. One-time purchase option available. Good alternative if you want a fresh interface.

🟢

Okular Free / Open Source

Linux-first, also available on Windows. Excellent for basic annotations on text PDFs. OCR support is limited — best used after you've already run OCR in another tool.

Frequently Asked Questions

Can I highlight a scanned PDF without OCR?

Not in the traditional sense. Without OCR, a scanned PDF has no text layer — the highlighter has nothing to attach to. Your only option without OCR is to draw a rectangle annotation over the area and set it to a semi-transparent yellow fill, which simulates a highlight visually but isn't tied to actual text.

Will highlights survive if I convert the PDF to Word?

It depends on the converter. PDF Agile's PDF-to-Word export preserves highlight annotations as Word highlight marks in most cases. Adobe Acrobat Pro also handles this well. Generic online converters often drop annotation layers entirely.

Is it safe to run OCR on confidential documents?

Yes — as long as you use a desktop app like PDF Agile that processes everything locally. Cloud-based OCR services (e.g., Google Drive's OCR, Smallpdf) upload your document to their servers. For legal, medical, or financial documents, always prefer an offline OCR solution.

How do I add sticky notes to a PDF that already has text?

You don't need OCR for text-based PDFs. Simply open the file in PDF Agile, go to the Comment tab, select the Sticky Note tool, and click anywhere on the page. The process is identical to Step 3 above — OCR is only needed for scanned (image) PDFs.

Conclusion

Here's a quick recap of the three-step workflow:

Run OCR — Tools → OCR → select language → Recognize. This unlocks the text layer on image-based scanned PDFs.
Highlight passages — Comment tab → Highlight tool → drag over text. Color-code by theme using the Properties panel.
Add margin notes — Use Sticky Notes for collapsible comments or Text Boxes for always-visible annotations. Save with Ctrl+S.

Once you've run OCR once, the result is saved inside the PDF permanently — you won't need to repeat it. Future editing sessions start directly at step 2.

🎯 Ready to try it? Download PDF Agile free at pdfagile.com — no account or subscription required. Then come back and read our next guide: PDF Annotation Guide for iPad and Windows Desktop.