The present paper reports the results of the relationship between the surface topography, microstructure and the in vitro bioactivity of samples with and without fluorapatite content in simulated body fluid. Glasses and glass ceramics belonging to the Li2O-SiO2-CaO-P2O5-CaF2 system were prepared by using conventional melting technique following by heat treatment to obtain glass ceramics. This current study demonstrates the benefits of combining two microscopic methods for better investigation of the surface structure. The formation of apatite layer on the surface and the increase in surface roughness proved that the glasses and glass ceramics with bioactive fluorapatite content could satisfy to the requirements for biomaterial applications. The results also showed that the roughness of apatite layer formed after immersion in body fluid on the surface of glasses with fluorapatite was more pronounced than that of equivalent glass ceramic samples cured under the same conditions.