© 2016, Springer-Verlag Berlin Heidelberg. Due to strong van der Waals (vdW) interactions, the graphene sheets and nanotubes stick to each other and form clusters of these corresponding nanostructures, viz. bi-layered graphene sheet (BLGS), double-walled carbon nanotube (DWCNT) and nanotube bundle (NB) or ropes. This research work is concerned with the study of nonlinear dynamics of BLGS, DWCNT and NB due to nonlinear interlayer vdW forces using multiscale atomistic finite element method. The energy between two adjacent carbon atoms is represented by the multibody interatomic Tersoff–Brenner potential, whereas the nonlinear interlayer vdW forces are represented by Lennard-Jones 6–12 potential function. The equivalent nonlinear material model of carbon–carbon bond is used to model it based on its force–deflection relation. Newmark’s algorithm is used to solve the nonlinear matrix equation governing the motion of the BLGS, DWCNT and NB. An impulse and harmonic excitations are used to excite these nanostructures under cantilevered, bridged and clamped boundary conditions. The frequency responses of these nanostructures are computed, and the dominant resonant frequencies are identified. Along with the forced vibration of these structures, the eigenvalue extraction problem of armchair and zigzag NB is also considered. The natural frequencies and corresponding mode shapes are extracted for the different length and boundary conditions of the nanotube bundle.