"High-energy and ultrafast soft/hard X-ray photon beams open new fields in Science with major applications to Biology, Chemistry and Physics. Indeed, a couple of X-ray free-electron lasers (XFEL) are under construction worldwide with the highly exciting objective to perform atomic resolution, 3D movies, by taking a sequence of femtosecond snapshots, of biological molecules such as viruses, proteins etc. Because of the need to capture an image on a single, femtosecond shot, the number of photons per shot should exceed 1013 and thus the intensity (≥ 1018 Wcm-2) on sample will far surpass any intensity ever achieved at short wavelength. Thus, the crucial question “will the structure of molecules be modified during the snapshot?” arises and has not been solved so far by lack of appropriate experiments. Non-linear effects may dominate and we are aware that we should control/understand theses processes. In 2009, the LCLS x-ray Free-electron laser at Stanford (USA) will be the first hard X-ray Free Electron Laser (FEL) in operation. The next one will be the XFEL in Hambourg in 2012. Our objective is to use the unique access to the Stanford XFEL through to study the interaction of ultra-intense X-ray FEL pulse with an aligned molecular ensemble. Complementary expertises in pump probe soft-X-ray and infrared light scheme in molecular science and theoretical support is provided through an international collaboration. This proposal requires the ultra-short duration to probe transiently aligned molecules and it needs the very high X-ray brightness to drive multiple ionization. We will distinguish between the linear (simple photo-absorption) and non linear response (two photon absorption) of the molecular system. We propose to use (double) core hole decay as a means of molecular orbital imaging. The diffraction of Auger electrons of the other atoms of a molecule offers a novel way to determine molecular structures."