MEMS used in inertial sensors rely on the movement of mechanical elements, generally systems of masses and springs. Shielding these structures from particulate contamination requires encapsulating the MEMS structures. This encapsulation is typically accomplished by placing a silicon cap over the MEMS at the wafer level. In the event the device stops functioning as expected, it is necessary to visually inspect the MEMS structures. However, once the device is capped, the only way to visually inspect the sensor is to remove the cap using a destructive decapsulation process. Fortunately, product analysts can take advantage of the transmissive properties of infrared light through lightly doped silicon to examine MEMS structures through their silicon cap using IR microscopy. Although useful, the image quality of conventional IR microscopy has limitations resulting from the optics, geometry and detectors currently available. Recently, laser confocal microscopy techniques have been adapted to the infrared spectrum, offering improved image clarity and measurement capability. This paper reviews the use of conventional IR microscopy in imaging through silicon caps, the limitations of conventional IR microscopy in this application, and the new capabilities afforded by the use of laser confocal IR microscopy for through-cap imaging.