The most commonly employed tools for wafer thickness and topography metrology are based on capacitance method, which due to physical size of probes, and may not be suitable for direct measurement of multi-layer non-conductive wafers or Micro Electromechanical Systems (MEMS) structures. Recently developed that low coherence interferometry provides solution, which overcomes limitations of these methods. Selected MEMS applications including characterization of deep (high aspect) trenches and membrane structures have been also developed. The above listed applications were limited to measurements of relative distance between two optical interfaces in material transparent at the wavelength of probing radiation. Absolute distance gauging by fiber optic low coherence interferometer is difficult due to large thermal drift (of the order of 0.04 mm/K). We demonstrate that this drift is a result of thermal changes of refractive index of fiber optic glass. We present solution eliminating this drift is based on introduction of the additional reference plane in the signal arm of the Michelson interferometer. Use of this reference plane eliminates influence of changes of refractive index of glass fibers on result of measurement and improves thermal stability of low coherence interferometer by three orders of magnitude.© (2005) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.