The routine application of electron microscopy in cell biology research has seen advances made in techniques that can capture information down to the organelle and membrane subdomain level. Correlative light and electron microscopy (CLEM) is one such technique that combines the modalities of light microscopy and electron microscopy using fluorescently labelled proteins. Here, we look at the technical application of CLEM in two different projects employing 2D and 3D approaches. 1) The first project involved the use of fluorescently labelled cross-linked and functionalized polymer nanoparticles to treat leukemia cells as a potential drug delivery system. Nalm-6 B cells were transfected with fluorescently tagged endosomal markers, treated with these fluorescent nanoparticles and their uptake and internalization within endosomal compartments imaged by confocal microscopy. CLEM was then used to look at these areas of interest within the cells to characterize the internalization and endosomal trafficking of these nanoparticles. This approach was useful as polymer nanoparticles are difficult to distinguish from their surrounding cellular components using routine TEM methods. 2) The second project analysed the immunological synapse (IS) formation upon activation of T cells to explore the function of specific fluorescently labelled protein cargos in close proximity to the IS. Here, super resolution airyscan confocal microscopy was used to capture the distribution of these proteins throughout the Z plane of individual cells and subsequently correlated at high-resolution with electron microscopy-based techniques. We performed 3D CLEM using both electron tomography of serial sections and plasma FIB-SEM. To improve visualization, an enhanced contrast en bloc staining protocol was used. Thus we were able to establish a validated workflow for 3D CLEM providing a novel approach.