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 MoS$_2$ particle 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 MoS$_2$ based particles directly from the friction track. The work contributes to advancements in both microscale manipulation and characterization. It also has implications for lubrication research