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We present an argon ion beam milling process to remove the native oxide layerforming on aluminum thin films due to their exposure to atmosphere in betweenlithographic steps. Our cleaning process is readily integrable withconventional fabrication of Josephson junction quantum circuits. Frommeasurements of the internal quality factors of superconducting microwaveresonators with and without contacts, we place an upper bound on the residualresistance 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 thetotal foot-print was exposed to the ion beam milling, in areas of low electricand high magnetic field, showed quality factors above $10^6$ in the singlephoton regime, and no degradation compared to single layer samples. We believethese results will enable the development of increasingly complexsuperconducting circuits for quantum information processing.

An argon ion beam milling process for native $\text{AlO}_\text{x}$ layers enabling coherent superconducting contacts