Pt-Pd bimetallic nanoparticles were characterized using aberration (Cs) corrected scanning transmission electron microscopy (STEM) along with molecular dynamics simulations. The nanoparticles were synthesized through a microwave-assisted process. This technique has been applied to synthesize metallic nanoparticles at relatively short times, allowing a good control of size distribution. The structure of the bimetallic nanoparticles is fcc-like with an average size of 5 nm. To understand the properties of the bimetallic nanoparticles, it is necessary to know the positions of all the atoms in the nanostructure. We have used a recent quantitative method to analyze HAADF STEM images which allowed us to measure the total intensity of the scattered electrons for each atomic column. Beside with the characterization of the nanoparticles, we have performed classical molecular dynamics simulation for the structural and dynamical analysis of the cuboctahedral Pt-Pd bimetallic nanoparticles.