We report on the Raman and photoluminescence characterization of three-dimensional microstructures created in single crystal diamond with a Focused Ion Beam (FIB) assisted lift-off technique. The method is based on MeV ion implantation to create a buried etchable layer, followed by FIB patterning and selective etching. In the applications of such microstructures where the properties of high quality single crystal diamond are most relevant, residual damage after the fabrication process represents a critical technological issue. The results of Raman and photoluminescence characterization indicate that the partial distortion of the sp3-bonded lattice and the formation of isolated point defects are effectively removed after thermal annealing, leaving low amounts of residual damage in the final structures. Three-dimensional microstructures in single-crystal diamond offer a large range of applications, such as quantum optics devices and fully integrated opto mechanical assemblies.