Adequate measurement of thickness of sheet-like materials or membranes is most important for quantifying their properties such as density, barrier properties and mechanical strength. Depending on the surface roughness of the membrane, the thickness measured by standard micrometre devices (apparent thickness) may considerably overestimate the actual geometrical mean thickness (intrinsic thickness) required for such purposes. In this work, we present a method for correcting the measured apparent thickness value of thin membranes for their surface roughness, thereby obtaining an improved estimate of the intrinsic thickness. The surface roughness data required for the correction can be obtained by common surface profiling techniques. The method includes a calibration parameter, the value of which can be found experimentally by independent measurements, or can be estimated theoretically using results from standard mechanical contact theory. The method is tested on a set of nanofibrillated cellulose films with varying roughness levels controlled by pulp fibre content. The surface topography of film samples was measured using laser profilometry, and the method was calibrated experimentally using data from X-ray microtomographic images for one type of film. The intrinsic thickness estimates given by the new method are generally in good accordance with independent results obtained from X-ray microtomography.