In this study, the morphological characteristics of the T. neapolitana biofilms on a ceramic carrier, stainless steel, graphite foil, carbon paper, carbon felt and carbon cloth using 3D reconstruction technology was investigated. This was based on the micrographs available in Squadrito et al. (Data Brief 33: 106-403, 2020). Besides the ceramic carrier, the other surfaces were conductive and slightly positively polarised (0.8 and 1.2 V). A simple drying technique was used to show the biofilm and avoid its detachment while chemical fixing with glutaraldehyde was used to better highlight the bacterial morphology within the biofilm. The latter was more suitable for investigating biofilm morphology while the former for bacteria morphology. For the ceramic carrier and stainless steel electrode surfaces, a regular undulating pattern of the biofilm was highlighted by the 3D rendering whilst the glutaraldehyde fixed sample showed a rod-like bacteria morphology. For the other surfaces, a regular undulating pattern of the biofilm and a mixture of a rod-like and a coccoid form of settled bacteria were evidenced also. Carbon cloth was the more suitable electrode for the current application due to its richer filamentous network of bacteria biofilm suggesting a better prevention of bacteria detachment from the electrode surface. Indeed, a preserved biofilm was highlighted on the surfaces of the polarised carbon cloth.