Here we report on two recent advances we made applying advanced fluorescence microscopy and spectroscopy to further the study of cell biology and drug delivery. At first, we detail a new instrumental set-up combining atomic force microscopy in liquid and super-resolution fluorescence microscopy in novel configuration such that long-term simultaneous and co-localized observation with both techniques becomes feasible. We believe this will contribute to the study of fast membrane activated cell-signalling processes in the years to come. Furthermore, we report on a novel application of fluorescence cross-correlation spectroscopy (FCCS) for the characterization of lipid-nucleic acid complexes. We could determine the number of nucleic acid particles incorporated in each liposome, a parameter not readily accessible on ensemble basis with other methods. This parameter is crucial for co-delivery applications, and we believe FCCS can play an important role in the future development of new drug delivery systems.