Island Southeast Asia (ISEA)is a key region for the study of human evolution. New fossil and archaeological evidence, from several islands, suggests an Early to Middle Pleistocene colonisation date by hominins. A taphonomic framework, however, such as that exists for Africa, is currently lacking, and taphonomical studies of ISEA vertebrate assemblages are very limited. In this paper, we apply multifocus and confocal microscopy to surface modifications on an Early to Middle Pleistocene avian assemblage from Mata Menge, in the So'a Basin of central Flores, Indonesia, with the aim of characterizing material and testing the relevance of 3D reconstructions to study the taphonomy of ISEA bone assemblages. Our observations document a number of bone surface modifications, including individual parallel grooves, overlapping spindle-like striations, elongated impacts, short composite grooves, and rows of pits. These features suggest that several taphonomic agents were at play during and after the accumulation of the Mata Menge small vertebrate assemblage. We find no unambiguous evidence for the exploitation of birds by the So'a Basin hominins, or for hominins being a significant accumulating agent of avian remains at Mata Menge. However, our work should be seen as preliminary, as direct comparative data on relevant biological agents are lacking. The markedly distinct faunal composition and climatic regimes of many Southeast Asian islands, and the potential use of different tools by hominins, warrants the development of a comprehensive taphonomical framework that is specifically relevant for ISEA.