Molecular self-assembly is emerging as a viable “bottom-up” approach for fabricating nanostructures. Self-assembled biomolecular structures are particularly attractive, due to their versatile chemistry, molecular recognition properties, and biocompatibility. Among them, amyloid protein and peptide fibrils are self-assembled nanostructures with unique physical and chemical stability, formed from quite simple building blocks; their ability to work as a template for the fabrication of low resistance, conducting nanowires has already been demonstrated. The precise positioning of peptide-based nanostructures is an essential part of their use in technological applications, and their controlled assembly, positioning, and integration into microsystems is a problem of considerable current interest. To date, their positioning has been limited to their placement on flat surfaces or to the fabrication of peptide arrays. Here, we propose a new method for the precise, three-dimensional patterning of amyloid fibrils. The technique, which combines femtosecond laser technology and biotin−avidin mediated assembly on a polymeric matrix, can be applied in a wide variety of fields, from molecular electronics to tissue engineering.