Capillary assembly in a topographical template is a powerful and flexible method for fabricating complex and programmable particle assemblies. To date, very little attention has been paid to the effects that the trap geometry-in particular the trap depth-has on the outcome of the assembly process. In this paper, we provide insights into the mechanisms behind this directed assembly method by systematically studying the impact of the trap depth and the surface tension of the suspension. Using confocal microscopy, we investigate the assembly process at the single-particle level and use these observations to formulate a simple mechanical model that offers guidelines for the successful assembly of single or multiple particles in a trap. In particular, single particles are assembled for shallow traps and moderate surface tensions, opening up the possibility to fabricate multifunctional particle dimers in two consecutive assembly steps.