In the context of finite element model updating using output-only vibration test data, natural frequencies and mode shapes are used as validation criteria. Consequently, the correct pairing of experimentally obtained and numerically derived natural frequencies and mode shapes is important. In many cases, only limited spatial information is available and noise is present in the measurements. Therefore, the automatic selection of the most likely numerical mode shape corresponding to a particular experimentally identified mode shape can be a difficult task. The most common criterion for indicating corresponding mode shapes is the modal assurance criterion. Unfortunately, this criterion fails in certain cases and is not reliable for automatic approaches. In this paper, the purely mathematical modal assurance criterion will be enhanced by additional physical information from the numerical model in terms of modal strain energies. A numerical example and a benchmark study with experimental data are presented to show the advantages of the proposed energy-based criterion in comparison to the traditional modal assurance criterion.