We calibrated and determined the measurement uncertainty of a custom-made Fourier domain short coherence interferometer operated in laboratory conditions. We compared the optical thickness of two thickness standards and three coverslips determined with our interferometer to the geometric thickness determined by SEM. Using this calibration data, we derived a calibration function with a 95% confidence level system uncertainty of (5.9×10(-3)r+2.3) μm, where r is the optical distance in μm, across the 240 μm optical measurement range. The confidence limit includes contributions from uncertainties in the optical thickness, geometric thickness, and refractive index measurements as well as uncertainties arising from cosine errors and thermal expansion. The results show feasibility for noncontacting absolute distance characterization with micrometer-level accuracy. This instrument is intended for verifying the alignment of the discs of an accelerating structure in the possible future compact linear collider.