To probe the structure and dynamics of molecules under optical trapping conditions, we exploit the effect of femtosecond Fluorescence Resonance Energy Transfer (FRET) between dye molecules coated on the surface of polystyrene microspheres of various sizes suspended in water. The use of femtosecond laser pulses enables sensitive detection through two-photon fluorescence (TPF). Unlike conventional backscatter signal, the TPF signal shows a slow counterintuitive decay for the trapped microspheres when they are not fully within the laser illuminated volume. This decay is a characteristic sign of the occurrence of the FRET process. For microspheres with sizes less than the trapping focal volume, trapping of multiple particles can occur leading to the formation of optically bound clusters. Using different laser polarizations, we also extract information about the structure and dynamics of such optically bound clusters as a consequence of FRET. (C) 2014 Elsevier B.V. All rights reserved.