The successful application of smart implantable devices requires materials used to easily adapt and respond to their microenvironment via physical and chemical cues. Nanotopography, a known important factor in cellular processes (i.e. cellular adhesion, proliferation, and, differentiation), has become a central approach to imparting clinically relevant materials with bioactive and biomimetic properties. This work focuses on the use of Directed irradiation synthesis (DIS), to create nanostructures on dissimilar materials including surfaces of metals, semiconductors, and polymers. DIS is a novel method that allows for the tuning of both surface nanoscale topography and surface chemistry through the tailoring of ion beam parameters, including energy and fluence. The application of DIS to direct cellular interactions on Ti6Al4V, MgAZ31, and PEEK is presented. Topography and chemistry changes at the nanoscale were characterized by SEM, XPS, AFM, and Contact Angle. In vitro tests were performed using macrophages (JJ741A) and human aortic and bone marrow mesenchymal stem cell (MSCs). DIS promotes an advanced cell adhesion state where cells are orientated following the designed nanofeatures in all irradiated specimens. A delay on immune response due to low levels of TNFa and higher levels of IL10 on irradiated Ti6Al4V were observed. Modified PEEK showed 3-fold higher ALP content at 7 days compared to pristine samples, and porous MgAZ31 treated with DIS revealed lower corrosion state and increased cell proliferation of HBMMSCs. Controlling the nanopatterning in biomaterials using DIS enables the design of bioactive surfaces to highly promote implant integration and tissue regeneration.