A fluid flow experiment was conducted on a granite sample containing two intersecting fractures. At constant confining pressure, water was supplied to the sample via a single inlet port, and the effluent was collected using four isolated outlet ports. The flow rate varied widely among these ports, indicating the formation of 3-D preferential flow paths (channeling flow), which likely occur in fractured rocks but have been considerably difficult to identify by existing methods. The novel concept of GeoFlow, a discrete fracture network model simulator in which fractures have a heterogeneous aperture distribution, has been developed to analyze such complex fluid flow. A fluid flow simulation was conducted using GeoFlow with aperture distributions within the two fractures, as determined using fracture surface topography data. Despite the simplicity of the simulation, GeoFlow revealed a 3-D channeling flow within the sample, which explains the general trend of the uneven outflows in the experiment.