  We present an argon ion beam milling process to remove the native oxide layer
forming on aluminum thin films due to their exposure to atmosphere in between
lithographic steps. Our cleaning process is readily integrable with
conventional fabrication of Josephson junction quantum circuits. From
measurements of the internal quality factors of superconducting microwave
resonators with and without contacts, we place an upper bound on the residual
resistance of an ion beam milled contact of 50$\,\mathrm{m}\Omega \cdot \mu
\mathrm{m}^2$ at a frequency of 4.5 GHz. Resonators for which only $6\%$ of the
total foot-print was exposed to the ion beam milling, in areas of low electric
and high magnetic field, showed quality factors above $10^6$ in the single
photon regime, and no degradation compared to single layer samples. We believe
these results will enable the development of increasingly complex
superconducting circuits for quantum information processing.
