A gas-cluster-jet generator with improved vacuum management techniques and apparatus is disclosed. The gas-cluster-jet generator comprises a substantially conically shaped vacuum chamber for housing the nozzle and jet exit portions of the gas-cluster-jet generator. A skimmer may be located at the narrow end of the conical chamber and a close-coupled vacuum pump is located at the wide end of the conical chamber. Support members for the nozzle are high conductivity “spider” supports that provide support rigidity while minimizing gas flow obstruction for high pumping speed. The conically shaped vacuum chamber redirects un-clustered gas in a direction opposite the direction of the gas-cluster-jet for efficient evacuation of the un-clustered gas. The nozzle and a skimmer may have fixed precision relative alignment, or may optionally have a nozzle aiming adjustment feature for aligning the gas-cluster-jet with the skimmer and downstream beamline components. Also disclosed are various configurations of gas-cluster ion-beam processing tools employing the improved gas-cluster-jet generator.