A method and an apparatus is provided for increasing biofilm formation and power output in microbial fuel cells. An anode material in a microbial fuel cell has a three-dimensional and ordered structure. The anode material fills an entire anode compartment, and it is arranged to allow fluid flow within the anode compartment. The power output of microbial fuel cells is enhanced, primarily by increasing the formation and viability of electrogenic biofilms on the anodes of the microbial fuel cells. The anode material in a microbial fuel cell allows for the growth of a microbial biofilm to its natural thickness. In the instance of members of the Geobacteraceae family, the biofilm is able grow to a depth of about 40 microns.