In microelectromechanical systems (MEMS), parallel plate structures with sub-micron separation have been of much use in various types of sensors and actuators. As the separation distance in these devices reaches down to hundreds of nm, it gets difficult to control the gap due to parasitic charging and the Casimir force. The Casimir force and its dependence on the boundary conditions of electromagnetic fields is a phenomenon that is mostly avoided rather than explored. In this paper, we present a methodology involving a micromachined parallel-plate geometry to measure the Casimir force at sub-micron separation. The new feature in this setup is the micromechanical means of parallelism control to measure the force at extremely small separation distances. A fabrication process for the micromachined parallel-plate structure is also given.