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Yes:
  1. atoms are smaller than molecules
  2. protons, neutrons, and electrons are smaller than atoms
  3. quarks are smaller than protons and neutrons
As best as can be determined by Particle Physicists at this time there is nothing smaller than quarks and electrons, as they act as mathematical point particles with zero volume in all experiments done so far. There are other subatomic particles of different types that also act as mathematical point particles with zero volume.

However a molecule is the smallest object that is a given chemical compound. Break it into smaller parts and it ceases to be that compound (it usually becomes other compounds having smaller molecules than the original compound).
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