This paper investigates the relationship between nanomaterials concentration, scaffold topologies, and mechanical and vibrational performance of additive manufactured Polylactic Acid (PLA) scaffolds reinforced with Graphene Oxide (GO) and Carbon Nanotube (CNT). Three different scaffold topologies namely Cube, Diamond, and Lattice Diamond were designed. Every scaffold comprised PLA reinforced with GO and CNT at different concentration levels of 0 wt%, 0.2 wt%, 0.4 wt%, and 0.6 wt%. The mechanical performance of scaffolds was evaluated via compressive testing. A representative volume element (RVE) model, evaluated using periodic boundary conditions, was developed and successfully validated against experimental results, with a deviation between 13.5 % to 23 %. The novelty of the work lies in incorporating GO and SWCNT agglomeration within the RVE models, enabling a more accurate comparison with 3D-printed composite test samples. Additionally, a comprehensive evaluation of scaffold shapes, geometry, vibrational response, and reinforcement concentration, provides valuable insights into their performance. Experimental and RVE results indicated that the PLAs reinforced with 0.6 wt% GO and 0.6 wt% CNT experience agglomerations. Finite element simulations using the Mooney-Rivlin hyperelastic model showed that the compressive strength of the structures followed this order: Diamond > Cube > Lattice Diamond. The results showed that increasing GO and CNT content from 0 wt% to 0.4 wt% led the Diamond scaffold to exhibit the greatest improvement in compressive strength and elastic modulus, with increases of 79.3 %, 26 %, 165.9 %, and 129 %, respectively. It was found that the additive manufactured modified PLA Diamond scaffold displays the best mechanical performance among the other scaffold topologies. The finite element analysis using the Lanczos Eigensolver revealed that mechanical enhancements and structural topology directly impact natural frequency variations, making them major parameters to consider for specific applications.