A versatile method for the directional assembly of M13 phage using amorphous carbon and SiO2 thin films was demonstrated. A high affinity of the M13 phage macromolecules for incorporation into aligned structures on an amorphous carbon surface was observed at the concentration range, in which the viral nanofibers tend to disorder. In contrast, the viral particles showed less freedom to adopt an aligned orientation on SiO2 films when deposited in close vicinity. Here an interpretation of the role of the carbon surface in significant enhancement of adsorption and generation of viral arrays with a high orientational order was proposed in terms of surface chemistry and competitive electrostatic interactions. This study suggests the use of amorphous carbon substrates as a template for directional organization of a closely-packed and two-dimensional M13 viral film, which can be a promising route to mineralize a variety of smooth and homogeneous inorganic nanostructure layers.