The radiation damage to a specimen in the chamber of electron microscopes has been studied extensively in the past few years. However, for the specific case of specimens with a core/shell structure, such as microcapsules and biological cells, there has been little experimentation devoted to understanding how the radiation may affect their mechanical properties. In the present work, single melamine formaldehyde (MF) microcapsules were imaged using an environmental electron microscope (ESEM) under both dry and wet modes under conditions of different accelerating voltages. The changes in the morphology (shape) were monitored as a function of radiation time. In addition, a newly developed ESEM based nanomanipulation technique was used to measure how the force imposed on single MF microcapsules for a given deformation changed with radiation time, in order to identify a time window within which the radiation damage to the microcapsules may be negligible in order to be able to study the mechanical properties of the particles. Based on the findings, the nanomanipulation technique was applied to measure the force versus displacement for compressing single microcapsules to rupture, including determination of their rupture mode.