Carbon nanotubes (CNTs) can be fabricated with an ordered microstructure by controlling their growth process. Unlike dispersed carbon nanotubes, these vertically-aligned arrays have the ability to support or inhibit bacteria biofilms. Here, we show that by treating the carbon nanotube arrays with plasma, different effects on biofilms of Gram-positive (Bacillus subtilis, Staphylococcus epidermidis) and Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa) can be observed.