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Annotating Files with the RemNote Reader
Annotating Files with the RemNote Reader

Read & highlight PDFs and other files within RemNote, then link parts of your documents to your highlights for easy attribution of sources.

Soren Bjornstad avatar
Written by Soren Bjornstad
Updated over a week ago

Once you've uploaded a file to RemNote, you can use the built-in RemNote Reader to highlight, annotate, and create notes and flashcards based on it.

Annotation is optimized for PDFs, but a wide variety of other files can be uploaded, including word-processor documents (.docx, .odt), slide presentations (.pptx, .odp), and text files. RemNote will automatically convert such files to PDFs so you can read and annotate them. You can also annotate web pages with the Web Reader. In this article, we’ll focus on PDFs, but other files will work similarly, and the web reader is similar as well (see its article for notes on the differences).

When you annotate a PDF, you’ll see a split-screen view, with the PDF on the right and a default document created for the PDF on the left. You’ll then read and highlight on the right as you paste and type notes on the left.


Highlighting is the main way to link your notes and flashcards to their sources. As you read, you’ll mark portions of the text (or other content) that you’d like to remember and attach references to these highlights to your notes.

Creating a highlight

To highlight text, hover your mouse over the text until the I-beam cursor appears, then click and drag to select the appropriate text. When you release the mouse button, the text will be highlighted.

In addition to these text highlights, you can create area highlights by holding down Ctrl (Cmd on a Mac), then drawing a rectangular box by clicking and dragging. Area highlights copy exact images of the selected area to your clipboard, so they're useful for capturing tables, figures, and other layout-sensitive elements of a PDF. Additionally, some PDFs (usually those that started life as a low-quality scan of a paper document) lack a text layer, which will prevent text highlighting from working; area highlights will still allow you to highlight in such PDFs.

If holding down Ctrl or Cmd is inconvenient for some reason, you can also switch to area highlight mode by clicking the pencil icon.

Using a highlight

When you finish making a highlight of either type, a reference to the highlight will be copied to your clipboard, and your cursor will leap into the other pane where your notes are displayed. You can now press Ctrl+V (Cmd+V on a Mac) to paste that reference, which will appear as an underlined version of the text of that highlight; clicking on it will take you to the location of the highlight in the PDF. (In the case of an area highlight, you’ll have a linked image instead of linked text.)

If you prefer, you can select Text or Pin from the menu that appears after pasting:

  • Text: Instead of pasting a reference to the highlight, paste it as plain text. Choose this option if you want to edit the text rather than displaying it exactly, perhaps to reformulate it as a better flashcard.

  • Pin: Rather than showing the full text of the highlight, show just a pin icon. When you click on the pin, you’ll jump to the location of the highlight. Ordinarily, you’ll put a pin in the same Rem as some other notes you’ve written.

It’s common to use Text and Pin together: First, paste as text and edit the text to create a flashcard or concise notes. Then, paste again and add a pin at the end of the text so you can trace this Rem back to its original source.

Highlight options

You can see more options for the highlight by clicking on it again.

From left to right, these are:

  • Copy: Copy a reference to the highlight which you can paste into your notes (this already happens automatically when you highlight something – use this option if you need to paste it again somewhere else later).

  • Highlight: Change the highlight color. The default choice, No Color In Editor, appears as yellow within the PDF and has no background color when you paste pins or quotes in the editor. The six colors to the right will both change the highlight color in the PDF and change the background color of pins and quotes.

  • Note: Attach arbitrary text to this highlight. You’ll see the text if you click on the highlight later or view it in the highlights pane, and you’ll be able to search for it from global search.

    This is not the primary way to take notes on a PDF in RemNote, however – normally you do that by typing in the other pane.

  • Link > Turn Into a Concept: Create a new top-level Rem marked as a Concept with the text of the highlight (as if you pressed Ctrl+Enter in a search), and add a portal to that Rem in your notes in the other pane. This is useful when you encounter new terms or ideas in your reading that you know will be relevant in many different contexts; rather than having to attach them to this specific document, you can add them in the context of your entire knowledge base from the start. (See Portals for more information on this workflow.)

  • Delete: Remove the highlight. Any references/links to the highlight in your notes will stop working, but they will show the title of the PDF and the text of the highlight after the words Deleted Rem, to be sure you don’t lose any information.

Contents and Highlights

Click on the sidebar icon in the upper-right corner of the PDF reader to view the table of contents and your highlights in another pane.

In the Contents tab, you can see all of the headings in the PDF and quickly jump to them by clicking on one. You can also copy the table of contents; if you paste this into your notes, you’ll have an instant outline you can take notes under!

In the Highlights tab, you can quickly view and edit all highlights you’ve made in the PDF so far.

Annotation options

You can find more options to customize the behavior of PDF annotation by clicking the … button on the toolbar.

  • Search in PDF (or press Ctrl+F): Search for text in the PDF.

  • Change theme: Set the PDF colors to dark, light, Solarized, inverted (swap black to white throughout the PDF, including on images), or the same as the current RemNote theme (see Dark Mode).

  • Auto highlight: This is on by default. If you turn it off, selecting text won’t create a highlight as it normally does; instead you’ll have to click the highlighter icon in the toolbar that appears after making a selection. If you’re trying to repeatedly copy text to somewhere outside of RemNote, this might be more convenient (although note that the Rem Reference copied when you create a highlight can also be pasted into other applications – you’ll get the text of the highlight).

  • Snap highlight to words: If turned on, you won’t be able to select individual letters within a word; the highlight will jump to the nearest word boundary. If you never need to select parts of a word, this will allow you to highlight faster by reducing the amount of care you need to take with where your cursor is pointing when you let go of the mouse button.

  • Edit highlight text: If turned on, when you click the Note option on the toolbar, you’ll be able to change the text of something you highlighted in addition to attaching additional notes. This may be useful if you have a PDF with a noisy text layer containing a lot of typos (for instance, one that was created by optical character recognition) – you can fix the text here so it doesn’t have mistakes in it when you paste the highlight elsewhere.

  • Split panes: By default, RemNote opens PDF annotation in a single pane with the PDF and a default document associated with the PDF together. If you want to take notes in a different document than this default document, turn on this option to split the view into two panes, then navigate to your chosen document in the left pane.

  • Download PDF: Click here to grab a copy of the PDF you’re annotating.

Keyboard shortcuts


  • Up/Down Arrow: Pan one line up or down;

  • Left/Right Arrows: Go to the previous or the next page;

  • Page Up/Page Down: Pane the file "one screen" Up or Down, respectively

  • Ctrl+F (Cmd+F on a Mac): Search text in the PDF

    • Enter, while using the search bar: go to the next search result

    • Shift+Enter, while using the search bar: go to the previous search result


  • Ctrl+C (Cmd+C on a Mac), after dragging to select some text: Highlight and copy the text.

    • If Auto Highlight is turned on, you will also copy the text after the highlight is created from dragging.

    • Pressing Ctrl+C (Cmd+C on a Mac), after selecting an existing highlight will copy that highlight.

  • N, after dragging to select some text: add a Note attached to that text.

    • If Auto Highlight is turned off, this will also add a colored highlight to the text).

    • You can also press N after selecting a Highlight to add a note to it.

  • Ctrl+drag (Cmd+drag on a Mac): Area highlight

  • Delete, after selecting a highlight: Delete the highlight

  • Ctrl+Alt+4-9 (Cmd+Opt+4-9 on a Mac), after dragging to select some text or an area: Highlight colors.

  • Ctrl+Alt+0: highlight with the "No Color in Editor" option.

    • This will be the same shortcut assigned to the "clear highlight" shortcut in the settings.


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