Measuring mechanical property is important in different scientific areas related to applications in macro, micro, and nanoscale devices. But unlike the microscopic measurements where numerous models are developed and tested, only a relatively very few approaches were tested nanoscale measurements. A special case includes indentation experiments for thin multilayered polymer systems. In this work, a model that describes the process of indentation in multilayered films with dimensions of several tens of a nanometer is developed and implemented in a software package. The software package is designed to work directly with files from atomic force microscopy data collected in Force Volume mode. The routine for the nanomechanical measurements of different multilayered polymer films was developed and it was shown that it is possible to receive reliable elastic modulus values and profiles. The model was tested for single hyperbranched molecules and polymer brushes, and model properties were investigated. It was found that in addition to elastic moduli behavior prediction, the model gives some estimation of the width of interfacial zone between adjacent layers.