In the present study, we explored plasmonic optical trapping (POT) of nanometer-sized organic crystals, carbocyanine dye aggregates (JC-1). JC-1 dye forms both J- and H- aggregates in aqueous solution. POT behavior was analyzed using fluorescence microspectroscopy. POT of JC-1 aggregates was realized in an increase in their fluorescence intensity from the focus area upon plasmon excitation. Repeating on-and-off plasmonic excitation resulted in POT of JC-1 aggregates in a trap-and-release mode. Such POT of nanometer-sized dye aggregates lying in a Rayleigh scattering regime (< 100 run) is important toward molecular manipulation. Furthermore, interestingly, we found that the J-aggregates were preferentially trapped than H-aggregates. It possibly indicates semi selective optical trapping of nanopartieles on the basis of molecular alignments. (C) 2017 Optical Society of America