An ion trap device comprises a wafer that supports at least one plate forming an ion trapping region therebetween. The plate has an electrically insulating surface and a multiplicity of electrodes disposed on the insulating surface. The electrodes form at least one ion trap in the trapping region when suitable voltages are applied to the electrodes via conductors coupled to the wafer. The device has a multiplicity of ports for introducing ions into the trapping region and for extracting ions from that region. In embodiments that include a multiplicity of such plates, a first one of the plates is oriented at a non-zero angle to the major surface of the wafer and is rotateably mounted on that surface. In one embodiment, at least two of the plates form an elongated micro-channel having an axis of ion propagation, and the electrodes on at least one of the two plates are segmented along the direction of the axis, thereby forming a multiplicity of ion traps along the axis. A controller applies suitable voltage (e.g., sequentially) to the segmented electrodes, thereby shifting ions from one trap to another. Preferably, the electrodes on the two plates are segmented. Applications to mass spectrometers and shift registers are described.