We present the methodology of computer modeling of an archaeological excavation. The method allows the study of archaeological formation, modification and transformation processes. Our main goal has been to build a computer model of midden-site formation processes. The main purpose of these models is converting excavation data to visual elements (lines, surfaces, and solids) which can be used as a representation of that data. Furthermore, geostatistics and other quantitative spatial analysis methods are also discussed to characterize the processes having generated the spatial distribution of archaeological data.