Bacteria in nature predominantly grow as biofilms on living and non-living surfaces. The development of biofilms on non-living surfaces is significantly affected by the surface micro/nano topography. The main goal of this dissertation is to study the interaction between microorganisms and nanopatterned surfaces. In order to engineer the surface with well-defined and repeatable nanoscale structures, a new, versatile and scalable nanofabrication method, termed Spun-Wrapped Aligned Nanofiber lithography (SWAN lithography) was developed. This technique enables high throughput fabrication of micro/nano-scale structures on planar and highly non-planar 3D objects with lateral feature size ranging from sub-50 nm to a few microns, which is difficult to achieve by any other method at present. This nanolithography technique was then utilized to fabricate nanostructured electrode surfaces to investigate the role of surface nanostructure size (i.e. 115 nm and 300 nm high) in current production of microbial fuel cells (MFCs). Through comparing the S. oneidensis attachment density and current density (normalized by surface area), we demonstrated the effect of the surface feature size which is independent of the effect on the surface area. In order to better understand the mechanism of microorganism adhesion on nanostructured surfaces, we developed a biophysical model that calculates the total energy of adhered cells as a function of nanostructure size and spacing. Using this model, we predict the attachment density trend for Candida albicans on nanofiber-textured surfaces. The model can be applied at the population level to design surface nanostructures that reduce cell attachment on medical catheters. The biophysical model was also utilized to study the motion of a single Candida albicans yeast cell and to identify the optimal attachment location on nanofiber coated surfaces, thus leading to a better understanding of the cell-substrate interaction upon attachment.