This paper reports on an exemplary study of the performance of commercial computational fluid dynamic (CFD) software programs when applied as engineering tool for microfluidic applications. Four commercial finite volume codes (CFD-ACE+, CFX, Flow-3D and Fluent) have been evaluated by performing CFD-simulations of typical microfluidic engineering problems being relevant for a large variety of lab-on-a-chip (LOAC) applications. Following problems are considered as examples: multi lamination by a split and recombine mixer, flow patterning on a rotating platform (sometimes termed ‘‘lab-on-a-disk’’), bubble dynamics in micro channels and the so called TopSpot(R) droplet generator for micro array printing. Hereby mainly the capability of the software programs to deal with free surface flows including surface tension and flow patterning of two fluids has been studied. In all investigated programs the free surfaces are treated by the volume-of-fluid (VOF) method and flow patterning is visualised with a scalar marker method. The study assesses the simulation results obtained by the different programs for the mentioned application cases in terms of consistency of results, computational speed and comparison with experimental data if available.