Snow cover area is dramatically decreasing across the Los Andes Mountains and the most relevant water reservoir under drought conditions. In this sense, monitoring of snow cover is key to analyzing the hydrologic balance in snowmelt-driven basins. MODIS Snow Cover daily products (MOD10A1 and MYD10A1) allow snow cover to be monitored at regular time intervals and in large areas, although the images often are affected by cloud cover. The main objective of this technical note is to evaluate the application of an algorithm to remove cloud cover in MODIS snow cover imagery in the Chilean Andes mountains. To this end, the northern region of Chile (Pulido river basin) during the period between December 2015 and December 2016 was selected. Results were validated against meteorological data from a ground station. The cloud removal algorithm allowed the overall cloud cover to be reduced from 26.56% to 7.69% in the study area and a snow cover mapping overall accuracy of 86.66% to be obtained. Finally, this work allows new cloud-free snow cover imagery to be produced for long term analysis and hydrologic models, reducing the lack of data and improving the daily regional snow mapping.