These experimental data are concerning the optimization of freeze-drying cycles of a model-type Casei probiotic bacteria with water based formulations using lactose and polymer polyvinylpyrrolidone (PVP) as cryo-/lyo-protectants. After a previous study devoted to the influence of the main freeze-drying parameters (freezing rates; shelf temperature; absolute pressure) on the bacteria survival ratios, this paper reports some morphological data obtained by scanning electron microscopy (SEM) with the final lyophilisates. The numerous and original SEM images realized with different formulations of water binary or ternary mixtures with fixed operating conditions proved to be very useful to explain and to understand the different bacteria survival ratios observed. Thus, with bacteria or micro-organisms systems, this powerful investigation method of characterization of lyophilisates morphology should be more largely used in the future for setting up the optimal formulations parameters (composition) and the connected operating physical parameters of freeze-drying steps (freezing rate, shelf temperature, absolute pressure).