You ask how electricity (electrons) gets through the mainly empty atom. That is a rather peculiar question. How would you expect an electron to get through a solid atom? After all, it is easier for us to walk through a mildly crowded space than through a crush, isn't it?
Note also that one must be very cautious in making statements about events at subatomic levels; an electric current, such as in a conducting wire, is not simply the same as moving electrons. It is the wave motion of the electrons, rather than moving the electrons themselves, travelling at the speed of light in the medium in question. Though the wave travels at the relevant speed of light, at typical voltages the electrons travel only millimetres per second.
You also ask whether a single atom can be regarded as the same element as atoms in a mass.
The answer is yes, certainly. Think carefully about the definition of an element; each element has an element number: hydrogen 1, helium 2, lithium 3, and so on up to uranium 92, and transuranic elements beyond. What those numbers represent is the number of protons in each atomic nucleus. Nothing else need be the same, but two atoms are of the same element if and only if that number is the same.
It takes tremendous energy applied in just the right way to change that number (for example by splitting a nucleus and sharing out the protons among the new nuclei) to change an element (we call that transmutation).
No such energy is applied in an atomic force microscope of the type you described.
So, once again, yes the single atom is still of the same element.