As annotations, drawing objects are placed by a drawing tool and can be selected by that same tool, or the Select or Hand tools. On flattening, they are removed from the Comments list and transformed to document objects that can only be selected and modified with the Edit Object tool.

To place an attachment as an annotation, click the Attach File or Attach Sound tool and click a page location. An icon appears; a tooltip shows the attachment name and author: double-clicking opens the file. Such attachments are listed in the Comments panel and the Attachments panel. On flattening, attachments are removed from the Comments and the Attachment lists. The file can no longer be opened, and only the icon remains showing where the attachment previously existed.

As annotations, text boxes are placed by the Text Box tool and can be selected by that same tool or the Select or the Hand tool. On flattening, text bpxes are removed from the Comments list and transformed to document objects that can still be read, but selected and modified only with the Edit Object tool.

As annotations, notes are placed by the Note tool. A double-click displays note text. On flattening, notes are removed from the Comments list and deleted; only the icon remains showing where the note previously existed.

As annotations, stamps are placed by double-clicking or drag-and-drop from the Stamps panel. Stamps can be selected by the Comment tools or the Hand tool. On flattening, stamps are removed from the Comments list and transformed to document objects that remain visible, but can be selected and modified only with the Edit Object tool. With the latter you are likely to select only one element from the stamp. Right-click and select Select Parent Group to select the entire stamp.

Layers are not annotations. They are listed or created in the Layers panel. On flattening with the Flatten dialog box, all layers are merged into one, with no undo facility. The Layers panel offers two commands: Flatten Layers and Merge Layers. Flatten Layers merges all layers into one, but Merge Layers lets you select which layers should be merged and which layer accepts the merged ones.

On flattening, deletions, highlights and other text markups remain visible, but can no longer be selected. Text that was inserted as new or replacement text is lost; only the insert symbol ^ remains to show where insertions were made.

On flattening, all form controls cease to be active and can no longer be selected with the Hand tool. They can only be selected and modified with the Edit Object tool.

On flattening, all 3D functionality is removed, the object becomes 2D, and can only be selected and modified with the Edit Object tool.

On flattening, the Movie ceases to be available, and only the icon remains visible where the movie previously existed.

When a file to be flattened contains real redaction, flattening the file conserves them. The black rectangles that block out redacted content can be selected and moved with the Select Object tool, but the removed content cannot be seen or searched. When a file to be flattened contains elements that are only marked for redaction, flattening the file does not conserve the redaction. The black rectangles that block out content marked for redaction can be selected and moved with the Select tool, but then the underlying content remains visible and searchable.