This paper examines the microstructure evolution of 3,4,9,10-perylene-tetracarboxylic bis-benzimidazole (PTCBI) thin films resulting from conditions imposed during film deposition. Modification of the silicon dioxide interface with a hydrophobic monolayer (octadecyltrichlorosilane (OTS-18)) alters the PTCBI growth habit by changing the unit cell contact plane. PTCBI films deposited on oxide surface have an orientation of (011), while films atop OTS-treated oxide surface have a preferred orientation of (001). The quality of the self assembled monolayer does not appear to influence the PTCBI growth preference significantly yet it enhances the carrier mobility, suggesting that charge traps are adequately passivated due to uniform monolayer coverage. High-quality monolayers result in n-type carrier mobility values of 0.05 cm2V–1s–1 Increasing the substrate temperature during PTCBI film deposition correlates with an increase in mobility that is most significant for films deposited on OTS-treated surface.