The morphology and pore arrangement of nanoporous anodic TiO2 arrays, prepared in the electrochemical cells with different sample alignments by the three-step self-organized anodic oxidation of titanium, were investigated at the bottom side of oxide layers. The quantitative analyses of pore spacing (cell size), pore density and pore arrangement were performed on the basis of FE-SEM bottom view images. The results show that the type of sample alignment and anodizing potential influence the pore spacing, pore density and pore arrangement. On the contrary, the anodizing temperature has a little effect on nanoporous anodic titanium dioxide (ATO) layers. Quantitative information on the nanopore arrangement, based on Delaunay triangulations, is also provided. The cells, which are not six-fold coordinated by neighboring cells, were recognized as defects and the percentage of defects, defined as a ratio between the number of defective pores and number of all pores on the analyzed surface was calculated for all the samples. A quite poor hexagonal arrangement with a relatively high percentage of defective pores (above 30%) was found for all studied anodizing conditions. However, the least percentage of defective pores suggesting the best nanopore arrangement was obtained for the potential of 60 V and 50 V at 10 °C and 20 °C, respectively.