The application of the focused ion beam (FIB) to the preparation of thin lamellae of Si-based samples for strain analysis by means of convergent beam electron diffraction (CBED) was investigated. The crystal damage induced by the ion beam at the sample surface is expected to influence the pattern quality strain analysis too. Repeatable results in the strain measurements were obtained only if a low energy (5 KeV) finishing step was used in the sample preparation. The strain measurement results obtained in patterned structures with different strain amount were also compared with the ones calculated using a commercial process simulator and with electrical measurements performed on the final devices.