We present a systematic comparison of the binary black hole (BBH) signal waveform reconstructed by two independent and complementary approaches used in LIGO and Virgo source inference: a template-based analysis, and a morphology-independent analysis. We apply the two approaches to real events and to two sets of simulated observations made by adding simulated BBH signals to LIGO and Virgo detector noise. The first set is representative of the 10 BBH events in the first Gravitational Wave Transient Catalog (GWTC-1). The second set is constructed from a population of BBH systems with total mass and signal strength in the ranges that ground based detectors are typically sensitive. We find that the reconstruction quality of the GWTC-1 events is consistent with the results of both sets of simulated signals. We also demonstrate a simulated case where the presence of a mismodelled effect in the observed signal, namely higher order modes, can be identified through the morphology-independent analysis. This study is relevant for currently progressing and future observational runs by LIGO and Virgo
