Laser micromachining is a powerful technique that is commonly used in microfabrication. Typically such laser systems are computer controlled, and the required microstructure is fabricated by multiple machining iterations, where the control program is modified until the required structure is achieved. Here a simple method of simulating an approximation of the surface topography that will result from a computer numerically controlled (CNC) laser machining program is presented for glass and silicon. The simulation allows rapid prediction of the etch depths, workpiece contours, resulting structuring and machining artifacts. It was found that the simulated surface topology closely matched that of the structures machined in each material (4% of the maximum etch depth for borosilicate, 7% for sodalime and 9% for silicon). A non-planar microfluidic channel system with through-substrate ports was produced in both types of glass and silicon. The design took 12 min to simulate and 74 min to machine, and the simulation was accurate to within 4 μm of the machined glass substrate.