Nanoscale systems combining colloidal quantum dots with plasmonic antennas will pioneer the development of novel nanodevices with tailored optical features for a wide range of applications. The interactions between such nanoparticles strongly depend on the particular distance. We propose the use of an atomic force microscope (AFM) to image and to position quantum dots with respect to plasmonic particles. Additionally, we analyze the arrangements with several optical characterization methods, such as confocal microscopy, fluorescence microscopy and superresolution optical fluctuation imaging (SOFI). These methods support each other and improve the AFM manipulation technique. The AFM tip is perfectly aligned to a focused laser by detecting the Raman signal of the silicon tip. Thus ultimately, we can simultaneously use the topography information with a spatial resolution in the range of the nanoparticle sizes and cross-correlate it with the optical characterization methods.