We report a novel microcolumn fabrication method using automated micro-electro-mechanical-systems (MEMS) assembly. Different microcolumn components, including deflectors, lens elements, and apertures, are fabricated on a highly doped 50 μm thick silicon-on-insulator (SOI) wafer. These components with compliant connectors are then assembled onto compliant MEMS sockets fabricated on the same wafer using MEMS NanoEffectors™ and automated assembly. The self-aligning nature of MEMS sockets yields submicron lateral alignment and less than 0.1° angular misalignment. The measured resonant frequency is 593 Hz for first generation assembled components; the footprint of the microcolumn is less than 1 cm2. We have successfully built a mechanical prototype microcolumn for technology demonstration and as a proof of concept. Second generation design is under development.