When using modal analysis to determine the building period do we need to use the stiffness modifiers (or in another word use the cracked section) to calculate the building period ? Can Anyone refer to any article or ACI reference that indicate anything related to this topic ?
Yes, you need to consider the effect of cracking on the stiffness of the building.
From Eurocode 8 (clause 4.3.1 (6)):
In concrete buildings, in composite steel-concrete buildings and in masonry buildings the stiffness of the load bearing elements should, in general, be evaluated taking into account the effect of cracking.
I don't have an ACI reference at the moment, but this NEHRP Seismic Design Technical Brief says in section 4.2:
When analyzing a special moment frame, it is important to appropriately model the cracked stiffness of the beams, columns, and joints, as this stiffness determines the resulting building periods, base shear, story drifts, and internal force distributions.