  Quantum bits (qubits) with long coherence times are an important element for
the implementation of medium- and large-scale quantum computers. In the case of
superconducting planar qubits, understanding and improving qubits' quality can
be achieved by studying superconducting planar resonators. In this Paper, we
fabricate and characterize coplanar waveguide resonators made from aluminum
thin films deposited on silicon substrates. We perform three different
substrate treatments prior to aluminum deposition: One chemical treatment based
on a hydrofluoric acid clean, one physical treatment consisting of a thermal
annealing at 880 degree Celsius in high vacuum, one combined treatment
comprising both the chemical and the physical treatments. We first characterize
the fabricated samples through cross-sectional tunneling electron microscopy
acquiring electron energy loss spectroscopy maps of the samples' cross
sections. These measurements show that both the chemical and the physical
treatments almost entirely remove native silicon oxide from the substrate
surface and that their combination results in the cleanest interface. We then
study the quality of the resonators by means of microwave measurements in the
"quantum regime", i.e., at a temperature T~10 mK and at a mean microwave photon
number $\langle n_{\textrm{ph}} \rangle \sim 1$. In this regime, we find that
both surface treatments independently improve the resonator's intrinsic quality
factor and that the highest quality factor is obtained for the combined
treatment, $Q_{\textrm{i}} \sim 0.8$ million. Finally, we find that the TLS
quality factor averaged over a time period of 3 h is $\sim 3$ million at
$\langle n_{\textrm{ph}} \rangle \sim 10$, indicating that substrate surface
engineering can potentially reduce the TLS loss below other losses such as
quasiparticle and vortex loss.
