A modular metrology apparatus comprises a vacuum chamber housing with an opening having a mechanical interface for sealed attachment of modular adapters. A sample stage inside the vacuum chamber positions a sample for processing. One or more charged-particle scanning systems scan particle beams across the sample. The mechanical interface enables integration of removable interchangeable modular adapters containing different configurations of process modules. The process modules are sealed within adapters and extend from outside to inside the vacuum housing towards the sample stage. Modular adapters are interchangeable to reconfigure installed process modules. Configurations may include scanning electron beams, focused ion beams, interferometers, detectors, and other process modules. The modular architecture provides a configurable mechanical framework to optimize the metrology apparatus by swapping adapters with customized sets of process modules.