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This article explores the challenges and solutions in the physical characterization of materials at the microscale using robotized systems, with a specific focus on manipulating and characterizing micrometer-sized particles with different and complex 3D shapes and internal sub-micrometer structures. In this paper, the studied particles are Molybdenum diSulfide (MoS2) based materials generated within the contact interface during friction. These particles are being studied because they offer a particularly promising solution for reducing mechanical friction and the associated high energy losses. However, they are distributed randomly within the contact area and possess intricate sub-micrometer structures. Characterization demands precise manipulation techniques in an in-situ Scanning Electron Microscope(SEM) environment. To address these challenges, existing commercial micro and nanomanipulation tools are integrated within a vacuum SEM chamber, and robotics strategies are investigated to enable the whole process from particle preparation, and manipulation setup definition, to effective MoS2particle characterization all in-situ SEM. A set of several complementary experimental investigations are done and involve force measurement and deformation estimation studies, leading to the first qualitative results on MoS2based particles directly from the friction track. The work contributes to advancements in both microscale manipulation and characterization. It also has implications for lubrication research.