This paper presents a 3D nanostructure modal vibration analysis by using finite elementmodels. The modal frequencies and corresponding modal shapes of silicon nanowires of various thickness against length ratios are determined by solving a linear structural eigenvalue problem for the 3D solid finite element model, where surface stress effects are taken into account by using the stress stiffness matrix. The cases of fixed/fixed and fixed/free boundary conditions at the nanowire ends are investigated. The results obtained by 3D solid models and models based on the beam bending theory have been compared with each other, as well as with the results obtained elsewhere in the literature computationally and experimentally. It has been shown that the effects caused by surface stresses are insignificant for wires with length-to-width ratio less than 10.