A high thermal conductivity of the underfill material is key for efficient heat removal from 3D chip stacks. Recently, the excellent thermal properties of underfills in which nanoparticle self-assembly formed necks between the filler particles were demonstrated. To industrially apply neck-based thermal underfills, the robustness of neck formation must be improved. Accordingly, it is crucial to understand the mechanisms of suspension drying in confined spaces. In this work, we present a study of particle self-assembly during colloidal suspension evaporation. The processes were directly observed by fluorescence imaging. In contrast to earlier work, particle self-assembly was studied not only within a model pillar array, but also inside a more representative filler-particle bed. First, microparticle assembly was investigated in porous cavities containing silicon micropillar arrays with different inter-pillar spacings. The 1-μm polystyrene particles used assembled by capillary bridging between the pillars. Pinning of the evaporation front at the outermost pillar row and particle transport to the cavity edges occurred. Accordingly, a large gradient in particle deposition was observed. The pinning could be mitigated by high evaporation temperatures, which led to fast propagation of the drying front. This resulted in directional bridging and a more uniform particle deposition. Moreover, a defect-free particle assembly on the millimeter scale was achieved by guiding the front with spiral pillar arrangements. Second, neck formation was studied in cavities filled with 250-μm filler spheres. In these particle beds, two evaporation stages were observed: vapor invasion along the larger pores and subsequent drying of the capillary bridges linking the filler particles. Homogeneous neck formation was obtained by evaporating a 1 wt% polystyrene suspension at 30 °C. Higher temperatures and concentrations both resulted in enhanced particle deposition at the cavity edges.