The best way is on your fingers. But you need a very small finger!
Quite precisely atoms can be „counted” by X-rays: they are diffracted on crystal planes, like the light on a CD disk. Thighter are placed the atoms – more distant are light spots on the screen. There are others ways of counting atoms (i.e. calculation of the Avogadro or Loschmidt number). For example as dependence of slime sedimentation in a liquid* (J. Perrin) or as dependence of their brewery** motion (A. Einstein). Today is possible to count on „fingers” leading it on the crystal surface. But... the finger must be quite small and precise. This finger can be a sharp tip of the tungsten needle – when it touches an atom (or better: approaching it, then needle gets slightly bent. Ask at the University - they will show you how it works***.
* Elements distribution of the slime with mass m in function
of height h is defined by formula e-mgh/kT ,where
k=R/NA is Boltzmann
constant.
** or better: Brown motions
*** Gdansk Technical University,
for example (and mamy, many other) are equipped with atomic force microscope.