In this paper, we describe a numerical method to model aperture structures and flow paths in single rock fractures based on actual fracture surface geometries and actual fracture permeability. Fracture surfaces were measured using a CCD laser displacement sensor (resolution: 10 μm) with 250 μm square mesh for 100 mm × 150 mm single tensile fractures in granite samples. Fracture permeability was also measured under 10-100 MPa confining pressure conditions. Aperture structures and flow paths were modeled numerically using the actual fracture surface geometries so that the model's permeability consistent with actual fracture permeability. Channeling flows were clearly observed at all conditions because of heterogeneous aperture structures. The results also suggested that fracture permeability could be overestimated if based on the conventional parallel plate model using an arithmetic mean value of local apertures.