Mesoporous nanocomposite materials have been fabricated through integration of evaporation-induced self-assembly and deep X-ray lithography. Micropatterned films made using a mesoporous ordered silica matrix which contains silver nanoparticles have been obtained. The exposure of the mesoporous films to high energy X-rays, which are generated by a synchrotron source, produces several effects: the removal of the surfactant, the densification of the silica backbone and the formation of silver nanoparticles. This integrated process produces a nanocomposite material which has a 2D-hexagonal organized porosity and silver nanoparticles with a sharp size distribution around 5 nm. The patterned nanostructured films have been tested as a lab-on-chip device for intrinsic surface enhanced Raman scattering detection using a solution containing rhodamine 6G in ethanol and measuring Raman response as a function of laser power.