Colloidal layers play an important role in environmental studies, for example in the movement of radionuclides in nuclear waste management. New characterization techniques are required for studying such complex, porous layers. The purpose of this work is to adapt coherence probe microscopy (CPM), which is typically used for measuring the surface roughness of single surfaces, to the analysis of thick inhomogeneous colloidal layers. Two types of layers, either composed of 80nm or 400nm alumina colloidal particles deposited on glass slides by decantation have been studied. One of the problems in performing routine roughness measurements of colloidal layers using CPM is the appearance of apparent pits below the level of the substrate surface. We demonstrate that this is due to partial detection of the buried colloid/substrate interface. Further, we have developed the "Z-scan" technique, which consists of building up an XYZ image stack by scanning the full depth of the sample. Any point in an XY image can then be investigated to study the local buried internal structure, layer thickness, and effective refractive index. Comparison of results with AFM and SEM confirm the structure found with CPM and the new "Z-scan" technique, which opens up new and useful applications. (C) 2010 Elsevier B.V. All rights reserved.