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The objective of this study is to develop the qualitative analysis of the low frequency Stoneley wave’s behavior in the borehole of the formation with the existence of fractures. The propagation of low frequency Stoneley waves in a borehole are modeled by using 1D finite difference time domain method. The propagation is investigated in the one layer formation with fracture then it is continued for the formation with various fracture aperture from the fracture zero velocity, 300m/s and 500m/s. It is concluded that the presence of fracture causes tube wave’s reflection and attenuation. While, the other modeling is set for VSP synthetic model in the condition 1 layer without fracture, 2 layer without fracture, 1 layer with fracture, 2 layer with fracture and 1 layer of formation with horizontal fracture intersecting the borehole. Results from the formation without fracture does not show any reflection, however, for 2 layer without fracture, the reflected waves are generated with also various noise waves. While, for 1 layer formation with single fracture, there is also a reflection but experiencing more attenuation than the 2-layer-unfractured model. And for the fracture intersecting the fluidfilled borehole, there are some movement towards the path of fracture to the left and right, and also into the borehole upward and downward. The modeling used in finite difference time domain are second-order hyperbolic system, while in VSP, the centered finite-difference method is applied.