An apparatus and a method for measuring very small separations between a transparent or semi-transparent first body and a second body, wherein one or more light sources produce light that is split into two distinct paths. One path is directed through the first body at two locations, one where it reflects from the interface at the separation to be measured, and another where the second body does not affect the reflection. The second path is directed at a frequency shifter, which shifts the frequency of the light. The two paths are recombined and interfereometric variations of intensity, substantially at the frequency of the shifter, are detected. The difference in phase between the measurement and reference areas with the second body not present is subtracted from the difference in phase between the measurement and reference areas with the second body present. The difference in differences yields the phase change that occurs when the second body is introduced. Using this phase change and the optical properties of the bodies and the medium between them, the separation is calculated. The preferred embodiment applies to the field of magnetic recording on hard disk drives and is used to measure the spacing or “flying height” between a transparent or semi-transparent replica of a magnetic recording disk and an actual recording head.