For many proposed applications of colloidal crystals it is desirable to obtain arrays with specific geometries. In this contribution, mechanisms competing with self-assembly during area specific deposition are identified and discussed. Specifically, flat chemically patterned substrates are created by micro-contact printing of alkanethiols and silanes. Polystyrene spheres (200–460 nm) are then deposited onto these patterned substrates by evaporative vertical deposition. The presence of a Rayleigh–Plateau instability and a stick–slip mechanism during area specific colloidal deposition are reported. It has also been demonstrated that when using the vertical deposition method, with patterned features of the scale 25–400 μm, difference in surface energy rather than electrostatic interactions dominate the direction of colloidal self-assembly.