Polydimethylsiloxane (PDMS) is used as a scaffold for cell culture. Because both the stress and strain acting on the substrate and the hemodynamic environment are important for studying mechano-transduction of cellular function, the traction force of the surface of a substrate has been measured using fluorescence images of particle distribution. In this study, deformation of the cross-sectional plane of a PDMS block was measured by correlating particle image distributions to validate the particle image strain measurement technique. Deformation was induced by a cone indentor and a shearing parallel plate. Measured deformations from particle image distributions were in agreement with the results of a computational structure analysis using the finite-element method. This study demonstrates that the particle image correlation method facilitates measurement of deformation of a polymer scaffold in the cross-sectional plane.