Heat dissipation in 3D chip stacks suffers from multiple thermal interfaces. The effective thermal resistance of the bond-line between individual dies, with the electrical interconnects can be minimized by the introduction of thermal conductive underfills. Up to now, only sequentially formed underfills result in true percolation and hence, thermal conductivities of more than 1 W/m-K. In this study, we report on various aspects to consider during the formation of percolating thermal underfills, by centrifugal filling of micronsized particles and the subsequent backfilling of an epoxy by capillary action. Particle assemblies within silicon-glass cavities were investigated for mono and poly-dispersed spherical and facetted particles with characteristic dimension in the range of 15 μm to 50 μm. Clogging of particles between silicon pillars could be mitigated at low particle fluxes dispensed by the hour glass principle. Particle shadowing behind the silicon pillars could be eliminated by ultrasonic agitation. Finally, close to crystalline phases could be identified for the mono-dispersed particles, compared to a random packing for the poly-dispersed particles. The effective pore diameter of the particle beds was experimentally derived from a backfilling experiment with viscosity standards. A normalized pore diameter of 0.15, 0.17 to 0.20 and 0.11 was observed for mono and poly-dispersed spherical and facetted particles, respectively. The backfill dynamics can be predicted with those values and the Washburn equation. Cavities filled with particles down to 30 μm diameter could be filled completely with the available low viscosity epoxy system. Finally, we report on the re-arrangement of filler particles due to capillary action and viscous drag, during the backfilling process. Defects are minimal for fluids of low surface tension and high viscosity. Hence, only 1 area-% of defects were observed from the infiltration of epoxies.