Flatten module

Flattening a PDF is the operation that permanently merges every layer and annotation into the content of each page. After flattening, annotations (watermarks, highlights, notes, drawings, forms, and so on) are no longer distinct from the document: they are part of the fixed image of the page. You reach this module from the Editing category of the Dashboard.

What is flattening for?

Several typical use cases justify flattening before distribution or archiving:

Securing annotations: preventing a recipient from removing a CONFIDENTIAL watermark, a Bates numbering or highlights;
Locking a completed form: keeping the values entered in an interactive form without leaving the possibility of changing them;
Preparing for printing: guaranteeing that the printed output will match exactly what is shown on screen, with no surprises from annotations that another reader might interpret differently;
Long-term archiving: eliminating interactive elements liable to age badly as the PDF standard evolves.

Flattening turns a "living" PDF (editable, interactive) into a "frozen" one (visually read-only).

Two complementary actions

The module offers two distinct operations, to be chosen according to your goal:

Flatten document

The main Flatten document button (at the bottom of the panel) starts the main operation:

every annotation is merged into the content of each page;
any layers (vector text, superimposed images) are also integrated;
form fields lose their interactive nature and their current values are frozen into the rendering;
a rotated page is flattened in its displayed orientation: the rotation is baked into the content, and the page takes the matching size (landscape for a quarter turn).

The text stays selectable; cropping, the document metadata (title, author…) and its outline are preserved.

After flattening, it is no longer possible to select, move or delete an annotation from HtkPDF or a third-party PDF editor. The operation is irreversible once the document has been saved.

Clean annotations

The Clean annotations button (in the Cleaning section) offers the opposite operation: deleting the editable annotations (notes, highlights, drawings) instead of merging them. The PDF returns to its original content, without annotations.

Use it to:

Quickly remove every annotation from a corrected document before returning it to its author (for example, deleting your proofreading notes);
Restore a clean version of a PDF that was accidentally annotated.

Unlike flattening, this operation does not alter the structure of the document: the pages, vector text and images stay unchanged. Only the annotations are removed — with two exceptions, links and form fields, which are part of the document and stay in place.

Confirming and history

Like any editing operation, flattening or cleaning:

creates a checkpoint in the History;
moves the document into pending changes;
only becomes permanent once it has been explicitly saved through the Save button on the Dashboard (⌘S).

Important: as long as you have not saved, you can step back through the History module or by leaving the document without saving. Once the PDF has been flattened and saved, the operation truly becomes irreversible — the annotations can no longer be restored.

Best practices

Always keep an archive copy of the unflattened document before saving the flattened version. This is a golden rule for being able to return to your annotations if needed (correction, update, version tracking).
Check the rendering after flattening: some annotations may differ slightly from their interactive appearance (positioning, shadows, transparency). Go through the pages before saving.
Combine with other security modules: for a document with controlled distribution, complete the flattening with a password (Protect module) and a metadata scrub (Scrubber module).
Flattening once is enough: there is no point re-flattening a document that has already been flattened. Annotations remaining after a first flattening are rare (save-time leftovers).

Note: flattening sometimes increases the file size slightly, because some vector annotations are rasterised. If the PDF size becomes a problem, run the Compress module afterwards to optimize the file.

Screenshots

1 screenshot — click to enlarge