Accurate measurement of Secondary Electron Emission (SEE) in scientific experiments provides better insight and understanding of field emission and multipacting properties in accelerator cavities. SEE properties of Niobium (Nb) are of significant importance to the performance and operation of accelerator cavities. Additionally, accurate Secondary Electron Yield (SEY) measurements from primary electrons generated from samples measured under different incident angles represent a technical challenge. For that purpose, the sample positioning system presented in this article is a design that allows for precise sample orientation and handling during single pump-down of the vacuum system in the experimental setup. Measurement techniques supported by a mechatronic system provide the means for acquisition of large quantities of data and at the same time reduce the experimental errors related to sample positioning. The authors describe a sample manipulation system and method for controlling the position of samples used for the measurement of SEY.