Rutherford's Nuclear Atom and Thompson's Plum Pudding Model were the two early models of the atom: Thompson models the atom as a jelly of electrons while in Rutherford model the atom is a nucleus surrounded by electrons. Thompson speculated that the atom contains thousands of electrons that make significant part of its mass.
Rutherford has proved his model by observing the Rutherford Scattering, how the thin foil scatters the alpha particles (positively charged nucleus of helium). A single alpha particle caused a slight fluorescence on the zinc sulphide screen. This screen was observed through the microscope, counting the flashes from the particles. The experiment accumulated data of thousands of flashes.
Some alpha particles have been deflected by very large angle or even bounced back. These large deflections cannot be explained by collisions with electrons that are 8000 times lighter than alpha particles ("It was almost as incredible as if you fired a 15-inch shell at a piece of tissue paper and it came back and hit you"). Rutherford concluded that particles hit something that is very small in comparison to the size of the atom yet much more massive than electron, first time suspecting the existence of the positively charged nucleus.
Rutherford also noticed that the golden foil deflects more particles than aluminium foil and successfully measured the relative size of the nucleus. Aluminium atoms are about ten times smaller so alpha particles hit them less frequently and less particles are deflected by the significant angle. This has much less effect on the small angle scattering.
These experiments mark the beginning of the nuclear physics.