To demonstrate, Dr Kim and Dr Weitz created what they call magnetic ink.
From the economist.com
Additionally specialty inks such as metallic, UV ink, magnetic ink, and more are available.
From the en.wikipedia.org
This means the counter will scan the ultraviolet properties of the bill and the magnetic ink in the bill at the same time it is counting the currency.
From the en.wikipedia.org
Because of the speed with which they can be read by computer systems, magnetic ink character recognition is used extensively in banking, primarily for personal checks.
From the en.wikipedia.org
In 1867 Lord Kelvin patented the syphon recorder, which recorded telegraph signals as a continuous trace on paper using an ink jet nozzle deflected by a magnetic coil.
From the en.wikipedia.org
They could perhaps do the same thing as the magnetic-impregnated paper currency without magnets, instead use raised areas of the paper or heavier ink in certain patterns.