In the submitted thesis, a novel combined approach of both focused ion beam (FIB) based target preparation and strain determination using electron backscatter diffraction (EBSD) in semiconductor nanostructures is presented. In the first part, a powerful cross-correlation algorithm for detecting small feature shifts within EBSD patterns and, consequently, determining the strain, is presented. The corresponding strain sensitivity is demonstrated using dynamically simulated diffraction patterns. Furthermore, novel procedures for automated pattern analysis are introduced. Results of systematic studies concerning the influence of ion species, ion energy and dose density on the surface quality of silicon surfaces are presented in the second part. For that matter, the assessment of surface amorphization and rippling is based on high resolution microstructural diagnostics (TEM, AFM, Raman) and molecular dynamics simulation. The high application potential of combined FIB preparation and strain analysis using EBSD is exemplarily demonstrated for a 60 nm thick sSOI-sample. The good agreement with established techniques like Raman spectroscopy and X-ray diffraction is also shown.