Intact liposome-based targeted nanoparticle delivery systems (NDS) are immobilized by non-selective binding and characterized by scanning probe microscopy (SPM) in a fluid imaging environment. The size, size distribution, functionality, and stability of an NDS with a payload consisting of a super-paramagnetic iron oxide contrast agent for magnetic resonance imaging are determined. SPM results are combined with information obtained by more familiar techniques such as superconducting quantum interference device (SQUID) magnetometry, dynamic light scattering, and electron microscopy. By integrating the methods presented in this work into the NDS formulation and manufacturing process, size-dependent statistical properties of the complex can be obtained and the structure-function relationship of individual, multi-component nanoscale entities can be assessed in a reliable and reproducible manner.