While most did pass through, Rutherford was shocked to find that:

Chosen because gold is incredibly malleable and can be beaten into a sheet only about 1,000 atoms thick.

To look inside the atom, Rutherford needed to fire something at it. He used:

A detector that would flash when hit by an alpha particle. The Unexpected Result

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Foil Experiment - Backstage Science: Rutherford Gold

While most did pass through, Rutherford was shocked to find that:

Chosen because gold is incredibly malleable and can be beaten into a sheet only about 1,000 atoms thick.

To look inside the atom, Rutherford needed to fire something at it. He used:

A detector that would flash when hit by an alpha particle. The Unexpected Result