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A methodology for determining long-term denudation rates from morphologic markers in a Digital Elevation Model (DEM) is checked by a comparative study of two drainage basins in the Precordillera of the Central Andes. In both cases the initial configuration of an incised pediment surface has been restored by using two different methods: the Black Top Hat (BTH) function and the Inverse Distance Weighting (IDW) interpolation. Where vertical incision and hillslope erosion are recorded, the 1DW appears to be the most adequate to reconstitute the pediment surfaces. Conversely, where only vertical incision is observed, the BTH describes more precisely the former pediment surfaces and it is easier to solve. By subtracting the DEM from the reconstructed marker we calculated an eroded volume, and estimated its uncertainty by considering Root Mean Square Error (RMSE) and DEM grid error. For the last similar to 10 Myr we obtained long-term denudation rates of 7.33 +/- 1.6 m/Myr in the San Andres drainage basin and 13.59 +/- 1.9 m/Myr in the El Salado drainage basin. These estimations are largely in agreement with other reported estimates of long-term denudation rates in the Atacama Desert. Comparison with long-term denudation rates reported in a wide range of climatic regimes suggests that our estimates cannot be explained by the current rainfall in the Precordillera. However they could be explained by a rainfall similar to that reported 40 km to the east in the Puna. This suggests that during the time span concerned the geomorphologic evolution of the study area, this evolution is dominated by an orographically controlled rainfall pattern. The preserved pediment surface and the small long term denudation rates determined in this study also indicate that the Precordillera was never reached by humid tropical air masses and precipitation as currently observed in the Altiplano during the summer months.