The repeated rubbing of a polymer microsphere against a hard, nanorough surface is a paradigmatic and not-so-simple process in tribology. Here, we have investigated this process in the case of poly(methylmethacrylate) (PMMA) colloidal probes (15 µm diameter) elastically driven on a Mo-doped DLC film with RMS roughness of about 3 nm in ambient conditions. The probes are flattened on length scales of few tens of nm, increasing with the applied load (up to few tens of nN). A complementary analysis on a periodic silicon grating enables a quantitative characterization of the early-stage nanowear process. On the Mo-DLC film, two different contrasts are observed, corresponding to the probe forming a multi-contact interface with the rough surface or sliding across the top asperities of the film. The contact area between probe and film, in the multi-contact regime, is also estimated based on the Persson theory. It allows us to confirm that the flattening of the sphere must be limited, with the applied loading force values, to a contact radius of about 750 nm.