This protocol describes a technique for picking individual nannofossils for geochemical analysis. The protocol allows for preparation of both individual nannofossil specimens and monospecific populations for analysis. A micromanipulator is adapted on an inverted microscope to hold a very fine tungsten needle capable of picking up individual selected nannofossils from an uncovered glass slide. Nannofossils can then be placed in designated areas on a Tacky Dot slide. Subsequently, they can be transferred to epoxy resin and disinterred from the Tacky slide. Nannofossils prepared using this protocol are suitable for subsequent analysis by secondary ion mass spectrometry. The preparation procedure in total takes 90–120 min per sample.