We present the methodology and the first results of a regional study of late pre-Hispanic occupation in the Azapa upper basin located in Arica y Parinacota region (ca. 3000 asl, Chile). The good preservation of the architectural remains in this mountainous region of the Atacama Desert allowed to perform effectively a survey by photo-interpretation of high-resolution multi-spectral satellite imagery. This aerial survey managed to duplicate the record of previously known late pre-Hispanic residential settlements in this watershed of 1000 km2. By developing a geodatabase that integrates this new information with abundant field-survey data, we document the extent and diversity of the late pre-Hispanic settlement pattern. It is confirmed that occupation was concentrated in three large residential complex located in the heart of the agricultural area. But the study also reveals an extended settlement pattern, with the identification of dozens of small settlements scattered in the region. These settlements are mostly estancias (small farms), which would be mainly associated to pastoral activities complementary with agriculture. We discuss the territorial function of these small farms and we propose that this type of settlement is potentially a good line of evidence to characterize the socio-territorial dynamics and macro-regional interactions occurred in the transect of 18°S between the Altiplano of Carangas and the Pacific Ocean.