Helium implantation in epitaxial thin films is a way to control the out-of-plane deformation independently from the in-plane strain controlled by epitaxy. In particular, implantation by means of a helium microscope allows for local implantation and patterning down to the nanometer resolution, which is of interest for device applications. We present here a study of bismuth ferrite (BiFeO3) films where strain was patterned locally by helium implantation. Our combined Raman, XRD and TEM study shows that the implantation causes an elongation of the BiFeO3 unit cell and ultimately a transition towards the so-called super-tetragonal polymorph via states with mixed phases. In addition, TEM reveals the onset of amorphization at a threshold dose that does not seem to impede the overall increase in tetragonality. The phase transition from the R-like to T-like BiFeO3 appears as first-order in character, with regions of phase coexistence and abrupt changes in lattice parameters.