Paleoclimatic glacial archives in low-latitude mountain regions are increasingly affected by melt, which leads to heavy percolation and can remove snow and firn accumulated across months, seasons or even years. Proxy system models, used for improved interpretation of glacial proxies and paleoclimatic reconstructions, generally do not account for melt because they are optimized for sites where snow layer removal by melting is negligible. In this paper, we present a mass balance model applied to the Mt. Ortles drilling site, at 3859 m a.s.l. in the Eastern Italian Alps, with the aim of building a pseudo proxy of atmospheric conditions during the formation of snow layers survived to ablation. This pseudo proxy is useful for improved dating and environmental interpretation of firn layers (<15 m depth), affected by significant melt in the period 1996–2011, which includes the extremely warm summer 2003. Here we show that the model significantly improves the interpretation of the firn stratigraphy. This is fundamental for detecting melted layers and for refining the dating of the core based on traditional annual layer counting of stable isotope and pollen seasonal oscillations.