We show that Ramsey spectroscopy of fermionic alkaline-earth atoms in a square-well trap provides an efficient and accurate estimate for the eigenspectrum of a density matrix whose n copies are stored in the nuclear spins of n such atoms. This spectrum estimation is enabled by the high symmetry of the interaction Hamiltonian, dictated, in turn, by the decoupling of the nuclear spin from the electrons and by the shape of the square-well trap. Practical performance of this procedure and its potential applications to quantum computing and time keeping with alkaline-earth atoms are discussed.