Apparatus and methods are disclosed for increasing the throughput of a charged-particle-beam exposure apparatus while maintaining alignment and exposure accuracy. The apparatus comprises a main chamber where exposure of sensitive substrates is performed using a charged-particle beam. At least one transport system moves and prepares the sensitive substrates for exposure in the main chamber. The transport system comprises at least one chamber. An evacuation device and a venting device are used to vary the pressure in the chambers as required. At least one switching valve is situated between the main chamber and a chamber in the transport system to isolate these chambers from one another. A flexible conduit connects the main chamber to the transport system. The apparatus and methods have especial utility for the processing of sub-micron level semiconductors.