This study presents a new planning approach within the context of the integration of archaeological and geological data in the planning process conducted in multi-layered cities. The modern urban physical space in multi-layered cities requires greater integration of natural elements through the use of the new advanced technology. Even though the archaeological cultural heritage/inventory is more recognizable in the urban space, the construction of modern cities increases the developmental pressure on the underground cultural heritage/inventory. This study seeks an alternative method for transferring the archaeological and geological data for the Preservation-Oriented Zoning Practice Plan by using the Geographical Information Systems (GIS), in accordance with the decisions on registering the cultural assets in Turkey. With this approach, the aim is to change spatial planners' perception of three-dimensional space and to propose a model for integrating archaeological data with the decisions based on the preservation plan. The effect of the elevation details of both the archaeological and geological data discussed on the integrated planning analysis and synthesis stage. The GIS were used for the spatialization of the archaeological data, while for the assessment and transfer of the obtained data by using ArcGIS software and 'georeferencing' and 'overlay analysis'. In addition, a field study was performed in Historical Peninsula, Tahtakale Region, and in-depth interviews and structured meetings were conducted with thirty-eight people to secure the contribution of different disciplines to the planning.