In this study, a novel methodology to measure the stiffness by point deflection of a flexible polymer layer suspended on liquid using a nano-indenter is presented. The measurement allows us to extract residual stress values of the polymer material using a simple analytical model. With this method, very low stress values can be obtained, of the order of 1MPa, with good repeatability. This method allows accurate mechanical behavior prediction and dimensioning of flexible membrane materials used in Microsystems devices.