They used many techniques, starting with shooting electrons through thin gold foil and noticing that while most of the electrons flew right through, some of them were deflected as if they had hit something hard. That’s how they discovered that atoms are mostly empty space with a nucleus. Then there is a technology called x-ray crystallography, where they were able to scan crystals and read the patterns to reconstruct the three-dimensional shape of the atoms in the crystal. That Parts too complicated to do an eli5 explanation.
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