Superconducting Quantum Interference Devices (SQUIDs) are highly sensitive magnetic flux detectors. We use scanning SQUID microscopy to investigate the behavior of vortices in the presence of locally applied strain. We induce mechanical strain with the tip of the SQUID chip and simultaneously map both the vortex configuration and the superfluid density. Our results suggest that the vortices strongly interact with local strain in Nb and NbN thin films. Further understanding of this interaction may lead to a new manipulation method of vortices as well as other nanomagnetic objects.