Scan
How to remove pen marks from a scanned document, without touching the print
Someone circled things in red, signed in blue across the text, or left a coffee ring. The printed words underneath matter. These methods remove the marks and keep the print, from the free trick that works surprisingly well to dedicated tools.
If you can rescan, use your scanner’s colour dropout setting to drop the pen colour. If not, the colour-channel trick removes coloured ink from black print in any photo editor: a colour looks almost white in its own channel. For stains, holes and mixed marks, brush over them with a tool that fills with the surrounding paper. Keep the original, and don’t clean marks from documents where they’re part of the record.
First: should you?
Removing a teacher’s corrections from your own worksheet or a coffee ring from an old manual is housekeeping. Removing initials, stamps, dates or notes from a contract, a medical record or an official form changes what the document says. Keep the original scan in any case, and if the cleaned copy goes to someone else, say it was cleaned.
1. Rescan with colour dropout
Many document scanners have a setting called colour dropout (or “drop out colour”) in their driver or scanning app. You pick red, green or blue, and the scanner treats that colour as white while scanning in grayscale or black and white. It’s the cleanest result possible, because the mark never reaches the file. It works best with clearly coloured ink on black print; dark blue ballpoint can be close enough to black to survive.
2. The colour-channel trick
Every colour image is made of three channels: red, green and blue. In each channel, ink of that same colour looks almost white, while black print stays black. So:
- To remove red pen, keep only the red channel.
- To remove blue ink, keep only the blue channel.
- Yellow highlighter is bright in both red and green; the red channel usually makes it disappear while the text under it stays.
In a photo editor that shows channels (Photoshop, GIMP, Affinity Photo, Pixelmator Pro), convert to grayscale using only that channel, or use a Channel Mixer set to 100% of that channel. Then raise the contrast a little with Levels so the paper becomes pure white. The result is black and white, which is what most scanned documents should be anyway.
It fails when the ink is dark, when the mark is the same colour as the print, or for stains, which have no single colour.
3. Healing and clone tools
For a few marks on an otherwise clean page, the healing brush or clone stamp in a photo editor copies nearby paper over the mark. It takes patience near text, because the tool can smear letters.
Newer “clean up” tools based on generative AI, including the one in Apple’s Photos app, are good at removing objects from photos. For documents, be careful: they invent what was under the mark. That can look plausible and be wrong, which is a real problem when the hidden thing was a digit.
4. Brush and fill with the paper
The safest approach for documents is the opposite of generating: paint over the mark and replace those pixels with the colour of the paper around them, while protecting anything that looks like black print. It can’t create a fake letter, because it only ever adds paper.
Putting it back into the PDF
If you cleaned page images in a photo editor, you’ll need to rebuild the PDF: export each page, combine them, and run OCR again so the text is searchable. Remember that removing a mark from the image doesn’t remove it from the OCR text layer, and an incremental save keeps the old image inside the file. If you’re removing something private, make a clean copy that rewrites the whole file.
Keepsign’s Erase marks works on the scanned page inside the PDF, on iPhone, iPad or Mac. Brush over a mark with your finger, Apple Pencil or mouse; with “Keep printed text” on, black and grey print under the brush is protected. Or remove all the blue, red, green or purple handwriting on a page in one tap, take away highlighter while keeping the words, and let it find punch holes, staples and fingers. It fills with the surrounding paper and never invents content. On our test page a coffee stain over form lines left 0.2% of its pixels and the text inside a red circle was untouched. Erase marks in Keepsign.
Sources
- How colour channels separate ink from print: standard RGB colour model; see any photo editor’s channel documentation, for example the GIMP User Manual, “Channels Dialog” (docs.gimp.org).
- Apple Photos Clean Up, described in third-party guides such as AppleInsider, “How to use Clean Up in iOS 18 Photos to remove distractions”.
- Keepsign measurement on a synthetic test page with known clean version, November 5, 2026.