In the development of new eco-cements for ecologically friendly construction, the porosity, surface structure and chemical nature of the material can influence the bioreceptivity of the surface and the aptitude or not of environmental micro-organisms to form biofilms. Such films are the source of biocontamination that can lead to a degradation in the structural properties over time. Accurate measurement of surface roughness and topography are important to help in the understanding of this interaction. Optical profilers are well adapted to the quantifying of large surface roughness typical of cementitious materials, being more rapid and better able to cope with high roughness compared with stylus and near field probe techniques. But any given surface profiler typically has specific range limits in terms of axial and lateral resolution and field of view, resulting in different roughness values according to the type of optical profiler used. In the present work, unpolished and polished cement paste samples have been measured with two different systems, one using interference microscopy and the other, chromatic confocal sensing. Comparison of the results from both techniques using the method of window re-sizing, more commonly used in tribology, has been used for calculating the average roughness parameters at different scales. The initial results obtained show a successful overlap of the results for the unpolished samples and a slight separation for the polished samples. The validation of the measurements is demonstrated together with a revealing of differences in the measurements on different types of surfaces due to variations in instrument performance.