Molecular dynamics simulations using empirical potentials are applied to characterize the structure, the energy relaxation and the stability of pyramidal-shaped quantum dots in the CdSe/ZnSe system. The relaxed structure models are used for a reliable interpretation of electron microscope investigations to analyze the size, the shape and the strain fields of the quantum dots. Though the elastic strains modify the electron microsope image contrast by creating virtual truncations of the pyramids or additional black-white lobes, optimum imaging conditions chosen will reveal the shape and the size of the dots.