Filling of liquid samples is realized in a microfluidic device with applications including analytical systems, biomedical devices, and systems for fundamental research. The filling of a disk-shaped polydimethylsiloxane (PDMS) microchamber by liquid is analyzed with reference to microstructures with inlets and outlets. The microstructures are fabricated using a PDMS molding process with an SU-8 mold. During the filling, the motion of the gas-liquid interface is determined by the competition among inertia, adhesion, and surface tension. A single ramp model with velocity-dependent contact angles is implemented for the accurate calculation of surface tension forces in a three-dimensional volume-of-fluid based model. The effects of the parameters of this functional form are investigated. The influences of non-dimensional parameters, such as the Reynolds number and the Weber number, both determined by the inlet velocity, on the flow characteristics are also examined. An oxygen-plasma-treated PDMS substrate is utilized, and the microstructure is modified to be hydrophilic. Flow experiments are conducted into both OPEN ACCESSMicromachines 2014, 5 117 hydrophilic and hydrophobic PDMS microstructures. Under a hydrophobic wall condition, numerical simulations with imposed boundary conditions of static and dynamic contact angles can successfully predict the moving of the meniscus compared with experimental measurements. However, for a hydrophilic wall, accurate agreement between numerical and experimental results is obvious as the dynamic contact angles were implemented.