A mechanical interlock system is reported that achieves the manual alignment of two components accurate to within +/-10 mu m in three spatial coordinates. In addition, the system allows rapid component interchange. The system is based on a novel two stage application of the principles of the kinematic location of instrument components. A macro scale kinematic mount allows manual handling while a micro scale mount delivers the accuracy required. Silicon microfabrication methods are used to create features in the micron size range accurately and repeatably for the micro scale mount. Such a system could be used for fluidic, pneumatic, electrical, optical, or mechanical interconnects. We use it for the alignment of optics to flow channel in an optical flow cytometer which is part of a microfluidic total chemical analysis system we are developing.