Understanding the mechanisms of biomineralization continues to be an important area of research in physics, chemistry, materials science, medicine, and dentistry due to its importance in the formation of bones, teeth, cartilage, etc. Stimulated by these fascinating natural examples, as well as by certain others such as shells and corals, attempts are being made to develop synthetic, biomimetic nanocomposites by simulating the basic principles of biomineralization. We have grown bio-like hydroxyapatite layers in vitro on substrates of stainless steel, silicon, and silica glass by using a biomimetic approach (i.e., immersion in a supersaturated simulated body fluid). Hydroxyapatite is one of the most common natural biomaterials and an important structural component of bones and teeth. Metal substrates are of interest for hard tissue implants, while semiconductors and glasses are under investigation for their use as biosensors. Using classical techniques such as stylus profiling, atomic force microscopy (AFM), and scanning and transmission electron microscopy (SEM and TEM), it was found difficult, ambiguous, destructive, or time-consuming to measure the topography, thickness, and profile of the grown heterogeneous, thick, and rough hydroxyapatite layers. On the other hand, coherence probe microscopy based on white light scanning interferometry and image processing provides rapid, contactless measurements of surface roughness and does not need any sample preparation. The results obtained have shown a typical layer thickness of up to 20 microm and an average root-mean-square (rms) roughness of about 4 mum. The hydroxyapatite investigated in this work presents nonetheless a challenge for this technique because of its semi-translucency, high surface roughness, and the presence of cavities formed throughout its volume. This results in a variable quality of fringe pattern, ranging from classical fringes (on a smooth surface) to complex fringes displaying properties of white light speckle (on a rough surface), together with multiple fringe signals along the optical axis in the presence of buried layer interfaces, which in certain configurations affect the axial and lateral precision of the measurement. In this paper we present the latest results for optimizing the measurement conditions in order to reduce such errors and to provide additional useful information concerning the layer.