Biofilms remain one of the most pervasive complications of the medical field, representing 50–70% of all nosocomial infections and up to 80% of total microbial infections. Since biofilms contain intricately small matrices, different microenvironments, and accumulations of biodiverse microorganisms of different resistances, these structures end up being difficult to target. As we review in this paper, 3D printing and nanotechnology help overcome these unique challenges of targeting biofilms, especially within the medical field. These technologies bring versatility and more precise control to personalized reusable medical device development and implants, with enhanced antimicrobial characteristics. They allow for decreased surface roughness of the implants, smaller pores, more targeted topography, and even added antibiotic or drug-releasing abilities for the medical devices. Furthermore, combining 3D with nanoparticles allows for the creation of anodized nanosurfaces of medical implants with increased osseointegration and reduced polymerization while promoting cost efficiency, durability, and biocompatibility. In this review, we explore the potentially valuable antimicrobial consequences of applying 3D technology and nanoengineering to dental and orthodontic implants, oral prostheses, hearing aids, joint replacements, catheters, stents, endotracheal tubes, prosthetics, and bone scaffolds.