Three-dimensional transient free surface flow into micro-channels was investigated both numerically and experimentally in this study. For the accurate modeling of interfacial movement, the developed fringe element reconstruction method was applied for handling not only an accurate treatment of material discontinuity but also surface tension across the interface and the contact angle at the contact line. The effect of surface tension was modeled by imposing tensile stress directly on the constructed surface elements at the flow front interface and the contact angle effect was considered by applying a capillary force directly to contact lines. The flow field was calculated by applying a mixed formulation based on a P1+/P1 tetrahedral element. Three channels which have similar planar geometrical shapes with the same thickness in three different dimensions were manufactured to observe the characteristics of micro-channel flow. The numerical results compared well to the experimental results in terms of the predicted shapes and positions of flow fronts.