Open a PDF and tap Drawing Tools (the pencil icon) in the reader toolbar. In Pencil mode, Apple Pencil draws. The native PencilKit palette provides pens, colors, stroke widths, an eraser, and lasso selection. Tap Done on the palette (or the toolbar button, when the palette does not cover it) to return to reading mode.
Apple Pencil is the default input. Finger touches continue to scroll and zoom the PDF in Pencil mode. A finger long-press on text leaves Pencil mode, selects the word under the finger, and opens the annotation menu, the same as reading mode. iPadOS offers no public API that reports when the Pencil is put away or attached to the iPad, so this long-press is the signal that you are back to reading.
In reading mode, Apple Pencil behaves like a finger: a long-press selects text and shows the highlight menu.
To draw without a Pencil, enable Draw with Finger in the reader's More menu. Turn Drawing Tools off to navigate or select text when finger drawing is enabled. The More menu also provides Undo Drawing and Redo Drawing for the active page's current editing session.
Drawings save automatically under Application Support/PDFMathReader/drawings, separately from highlights and translations. Local saves follow the source file's URL, so highlighting and rewriting the PDF does not orphan its drawings. Renaming or moving the source file outside the app changes that local association; export and reopen the exported PDF to carry editable drawings to a new location.
Original, translated, and AirDrop exports include both a standard PDF stamp appearance and the original PencilKit data. Other PDF viewers can display the appearance; reopening the exported file in PDFMathReader restores editable strokes. Exported appearances are rasterized at twice PDF point resolution; editable strokes retain their pressure, masks, and tool data.
Validation includes iPad simulator palette interaction, saving/reopening/erasing, corrupt sidecar protection, and PDF appearance/data round trips. Apple Pencil hardware input, palm rejection, and accessory gestures require a physical-device check.