Harmonic excitation of structures caused by rotating equipment is a problem faced by many engineers in the field of Operational Modal Analysis (OMA). Several methods to discard the influence of harmonic inputs over systems natural responses has been proposed in the literature and implemented in various software solutions. This paper recalls some of the most used techniques and uses a new time domain method for removing harmonics from measurements. Deployed method does not rely on filtering, statistical detection nor on non-linear fitting. Instead, it predicts the harmonic part of the time series and deploys an orthogonal projection of the latter onto the raw measurements to remove the harmonic part of the signal. The new technique is a part of an semi-automated framework for OMA of structures contaminated with harmonics, whose flow is presented in this paper. The merit of the framework is discussed in the context of OMA of a full scale operating ship with rotating machinery on-board.