In the design of the substructures of the buildings, very innovative and at the same time sigificant changes had taken place during the Cobble Paved Building Subphase; the rather complicated raised flooring system was given up. Changes in architecture that took place during the Cobble Paved Building Subphase are not restricted to the substructures of the buildings; the planning concept of the building has also been modified. The new layout is a tripartite arrangement of rooms that are connected by door-like passages. The buildings are finished by paving the floors with cobbles (sometimes these are also plastered). Small buttresses against the walls, insides and outside, might have helped support the roof. Towards the end of the Cobble Paved Building Subphase the rooms of some of the buildings had become smaller almost identical to those of the early cell buildings and the buttresses had lengthened into walls. Although there is a lack of evidence about roofing systems, the cobble paved buildings was suitable for supporting a flat roof. Buildings that had been one storey prior to the time of the Cell Building Subphase now become two storey. This layout not only provided dry living space but also extra interior space for functions such as storage, graves, etc. The interior divisions of the basements are sometimes on the short, sometimes on the long axis. The upper storeys, which are constructed with long rectangular kerpic blocks, are separated from the basements by thick earthen floors. The arrangement of the upper living floors is not clear but a few elongated kerpic blocks indicate the presence of separation walls. The rush or reed mats used mainly are presumed to have also been used as division walls. Both the house models and burnt kerpic fragements with beam impressions attest to heavy flat earthen roofs with a parapet around them. These flat roofs also provided a large utility area for the Cayönü people living in the same "buildig isula". The upper floors are reaced by wide stone steps on the northeast end of the sidewalks encircling the buildings. To reach the roof a ladder was possibly used. Some buildings of the second phase (c2) were constructed without the stone socles. In the western sector, all the buildings of this phase are heavily burnt. One of these buildings had a single room surrounded by kerpic walls on stone socles with a sunken floor level, no substantial divisions, the presence of large plastered storage baskets (bin-like constainers) and a clay bench. This mudbrick bench is the coffin of a flexed woman wrapped in a mat. A tool kit, possibly in a pouch, had been left by the body. The general appearance of the village of the CP-Subphase of the Third Evolutionary Stage is quite different from that of the Channeled Building Subphase. The open areas diminish in size (without a change in function), and there is a tendency to enclose the open spaces resulting in the closed countryards between the buildings of the Late Cell Building Subphase. In the first two phases (c1-2), the domestic buildings in the eastern sector of the settlement were located around the western end of the Pebbled Plaza of the Cobble Paved Building Subphase, whereas in the last phase (cp3) the Pebbled Plaza is enlarged towards the west and domestic buildings are constructed only in the north. 
In the Cell Building Subphase in the western sector, the buildings are constructed along two or three paralel stone terraces of different heights, with little "closed courtyards" (ca. 55m2) between them. A similar pattern is observed in the northern half of the eastern sector of the village. The workshops and working areas move further west to the open areas between the more scattered buildings. In this period, tempered clay was more used as a construction material. The tradition of burying buildings is more evident, especially in the early cell buildings. Cell doorways were blocked with stones and earth; ground stone objects, animal bones, and edible plants were left in the buildings, personal items were removed before the buildings were burned down and filled with their burnt rubble. In the eastern sector this tradition gave opportunity for a large area covered with stones to turn into the first Pebbled Plaza, a forerunner of the Earth Plaza of the Cell Building Subphase, the first of the tradition of special open areas, and a phenomenon which made the division of the settlement into functional areas more prominent. During the Phases cp1-2 the Pebbled Plaza had houses to the north and west, in cp3 it enlarged westward and domestic buildings were to be found only to the north. The Pebbled Plaza is bordered by special buildings to the south: the rectangularly planned Skull Building (BM2) with the single roomed building (BL) annexed to it and the Bench Building (BK) with a pebble paved floor and benches running along its walls on three sides. Its southern wall was constructed on the northwall of the buried Flagstone Building (FA, see settlement Second Stage). No workshops/workareas have been found at the plaza, it was used only for daily activities and perhaps also special ceremonies and was renewed at least three times. The renewals-fill became the foundation of the Earth Plaza of the Cell Building Subphase (c1). The Earth Plaza has a reddish floor, which was renewed many times and carfully cleaned before each renewal. The earliest Plaza had two parallel rows of standing stones (uncarved stelae); two grooved limestone slabs lay close o each other. All these stones and slabs were intentionally broken and buried during the second renewal of the floor. To the north of the Plaza were the houses of the elite and to the northeast was the Terrazzo Building (c1). The latter is constucted of wide stone walls with two small buttresses, which seem to have a special meaning over and aboe that simply supporting the wall, placed opposite each other. The floor is made of pinkish-colored limestone, which was poored (probably crushed) onto a fill of white limestone chips mortared with slaked lime; the surface was later flattened by burnishing, water was probably used as a levelling agent. Two lines of white stones were made on the red floor, aligned with the buttresses. In the northeast corner of the building ther is a lunar "hearth" opening towards the northeast. The building was abandoned after the central part of the floor was destroyed, but a quarter of a shallow basin with a stylized human face in low relief on its side was left behind. A new rectangular Skull Building (BM2) was set in the fill of the BM1 buildings and was in use during the entire span of the Cobble Paved Building Subphase (cp1-3). It has two sections, there are three interconnecting rooms (in its first phase four rooms) in the north, and a large rectangular flat stone, perhaps a funeral stone or an altar, oriented north-south and placed near the west wall. In phase c of this building, these two sections were separated from each other by a kerpic bench in which were two standing stones (from one of the BM1 buildings?) were buried. The "altar" was destroyed and fragments used as building materials in different parts of the following phase. Whether there was a south wall to the courtyard is not known since the part was totally destroyed by the Bogazcay and the Early Bronze Age terracing for metal working. In the three-roomed BM2b Building phase, the rooms and the courtyard were separated from each other by raising a stone wall on the kerpic bench of BM2c. With its thick and high walls, buttresses on the outside of the south wall, facing the courtyard, stone paved rooms, and well burnished pink funeral stone or an altar, the final Skull Building (BM2a) appears to have been a monumental building. After its destruction (intentional burning, filled with its own rubble, buried under a layer of pebbles) the Terrazzo Building was built to the north of the area, domestic buildings to the southeast. The northeast corner of the Skull Building was destroyed by a deep well/hole with a stone surround from a much later period.
