The discrete fracture network (DFN) model simulation, in which the fracture network can have a natural heterogeneity, is one of the most effective approaches in fluid flow analyses for a fractured reservoir. In the DFN model simulation, the fracture is modeled by a pair of parallel smooth plates although real fractures have rough surfaces. However, numerous field and laboratory observations have suggested that fluid flow through a fracture occurred in specific preferential flow paths (channeling flow) due to a heterogeneous aperture distribution formed by the rough surfaces. The conventional DFN model simulation therefore gives us a serious concern about the reality. To address this concern, we have developed a new concept DFN model simulator, GeoFlow, in which the fracture can have the heterogeneous aperture distribution. Three dimensional fluid flow simulation was performed for a simple fracture network by both the conventional and the new concept DFN models. In the conventional DFN model simulation, the fracture had no aperture distribution, and fluid flow in the fracture plane was quite uniform. On the other hand, the GeoFlow simulation showed formation of three dimensional preferential flow paths in the fracture network. In addition, another GeoFlow simulation showed that productivities of the wells highly depended on their locations even when the wells intersected the same fracture. The productivities were considerably smaller when the wells intersected the regions with smaller aperture conductivities, where the preferential flow paths were difficult to form at the natural condition (no well condition). The results demonstrated occurrence of three dimensional channeling flow in fractured reservoirs, which should be addressed for effective developments of the reservoirs.