Buildings with complex geometries often present challenges in dynamic identification due to the presence of numerous vibration modes, some of which are closely spaced and difficult to clearly identify. These modes can be hard to differentiate during modal testing, which can create complications when tests are performed at different times. This study addresses the challenges encountered in the dynamic identification of a complex hospital building using operational modal analysis. The building consists of several structural bodies of the same height and structural typology, built adjacent to each other, resulting in a complex floor plan geometry. Additionally, the entire structure underwent seismic retrofitting, with the once separate bodies now interconnected by steel elements and dissipative devices. The issues in the comprehensive dynamic identification are addressed, and a procedure for the definition of a reference sensor configuration for ambient vibration tests on such buildings is proposed.