Focussed ion beam (FIB) milling can be used to reveal sub-surface fracture and deformation below indents in materials. However, evolution of residual stresses around the indent impression cause changes to the crack morphology during the FIB cross-sectioning procedure. Berkovich nanoindents in single crystal hexagonal (6H) silicon carbide cause radial surface cracks, and the residual stresses are mapped using Raman piezospectroscopy and high angular resolution EBSD. FIB milling changes the stress state, allowing surface cracks to extend, and sub-surface cracks to evolve, precluding direct observation of sub-surface crack morphology using this technique. Raman spectroscopy after FIB milling reveals that the compressive residual stress has been relieved allowing crack extension. Ion irradiation damage subdues cracking in 6H-SiC, and differences in residual stress maps explain the role of cracking in relieving residual tensile hoop stress around indents.