Cultural heritage (CH) documentation tasks usually involve professionals from different knowledge areas, which implies not only a huge amount of information and requirements, but also a very heterogeneous set of sources, data structures, content and formats. Geographic information systems (GIS) have been used extensively by cultural heritage specialists, but this is just working around the real problem: there is no specialized software for CH professionals to document their work in 3D. In this paper, we present software named Agata that allows specialists to interact in real time with high resolution polygonal models, and to annotate different raster and vectorial information directly onto them that might be useful for current or future research. Moreover, these annotations can be exported in a standard format that allows researchers from other disciplines that might be interested in the dataset to access such information easily. The system is able to manage and annotate not only on buildings or archaeological sites, but also sculptures or paintings directly into the 3D dataset of any CH physical element.