n recent years, tomographic 3D reconstruction approaches using Electrons rather than X-Rays have become popular. Such images produced with aTransmission Electron Microscope (TEM) make it possible to image nanometer-scale materials in 3D. However, they are also noisy, limited in contrast, and most often have a very poor resolution along the axis of the electron beam. The analysis of images stemming from such modalities, whether fully or semi automated, is therefore more complicated. In particular, segmentation of objects is difficult. In this article, we propose to use the continuous maxi- mum flow segmentation method based on a globally optimal minimal surface model. The use of this fully automated segmentation and filtering procedure is illustrated on two different nano-particle samples and provide comparisons with other classical segmentation methods. The main objectives are the measurement of the attraction rate of polystyrene beads to silica nano-particle (for the first sample) and interaction of silica nano-particles with large unilamellar liposomes (for the second sample). We also illustrate how precise measurements such as contact angles can be performed.