The dependence of the orientation of microscale PS cubes, which are surface functionalized on only five faces, at the water/air interface and the ordered aggregates formed by capillary force assembly are reported. Depending on the wettability of the faces, the cubes were shown to adopt a preferred orientation that changes with decreasing wettability from face up to edge up and further to vertex up. Concomitantly, stable aggregates with different structures were formed by capillary force self-assembly. The unmodified bottom face of the cubes was localized by fluorescence labeling. Finally, self sorting of differently surface functionalized microcubes was realized for the first time, due to the stronger capillary interactions of quadrupole-quadrupole and hexapole-hexapole interactions compared to quadrupole-hexapole interaction.