A system and method for controlling a tunneling current between a first element and a second element of a micro-electro-mechanical system (MEMS) sensor. The system includes a tunneling current excitation source for providing a tunneling current between the elements and a tunneling current monitor for monitoring a change in the tunneling current responsive to movement of at least one element. The system also includes a positioner for positioning at least one of the elements and a controller in communication with the tunneling current monitor for controlling the positioner to position at least one of the elements at a first spacing between the elements for configuring the system in a referencing mode; and to position the elements at a second spacing for configuring the system in a sensing mode, whereby the system is calibrated with respect to the referencing mode.