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Indentation is a common experimental technique to study the mechanics of polymeric materials. The main advantage of using indentation is because this provides a direct correlation between the microstructure and the small-scale mechanical response, which is otherwise difficult within the standard tensile testing. Here, majority of studies have investigated hydrogels, microgels and/or elastomers. However, a lesser investigated system is the indentation in highly cross-linked polymer (HCP) networks, where the complex network structure plays a key role in dictating their physical properties. In this work, we investigate the structure-property relationship in HCP networks using the computational indentation of a generic model. We establish a correlation between the local bond breaking, the network rearrangement, and the small-scale mechanics. The results are compared with the elastic-plastic deformation model. HCPs harden upon indentation.