Rutherford's experiment indicated that matter was not as uniform as it appears what part of his experimental results implied this idea

Rutherford theorized that atoms have their charge concentrated in a very small nucleus.

This was famous Rutherford's Gold Foil Experiment: he bombarded thin foil of gold with positive alpha particles (helium atom particles, consist of two protons and two neutrons).  

Rutherford observed the deflection of alpha particles on the photographic film and notice that most of alpha particles passed straight through foil.

That is different from Plum Pudding model, because it shows that most of the atom is empty space.

According to Rutherford model of the atom:

1) Atoms have their charge concentrated in a very small nucleus.

2) Major space in an atom is empty.

3) Atoms nucleus is surrounded by negatively charged particles called electrons.  

4) An atom is electrically neutral.