A Micro-Electro-Mechanical System (MEMS) apparatus provides for self-calibration of mirror positioning of a moveable mirror of an interferometer. At least one mirror in the MEMS apparatus includes a non-planar surface. The moveable mirror is coupled to a MEMS actuator having a variable capacitance. The MEMS apparatus includes a capacitive sensing circuit for determining the capacitance of the MEMS actuator at multiple reference positions of the moveable mirror corresponding to a center burst and one or more secondary bursts of an interferogram produced by the interferometer based on the non-planar surface. A calibration module uses the actuator capacitances at the reference positions to compensate for any drift in the capacitive sensing circuit.