The CIEMic was originated in 1974, first like the Electron Microscopy Unit (UME) in response to the need of researchers from the University of Costa Rica to have electron microscopy equipment. These equipment were donated by the Government of Japan through the Japan International Collaborative Committee (JICA). Moreover, the UME established a cooperative agreement with the government of Japan that allowed developing a training program for Costa Rican and Latin American researchers in electron microscopy techniques.

Initially, the UME was located as a unit assigned to medical school, but in response to increasing development of different lines of research that use high resolution microscopy, in 2001, the UME became in the Research Center in Microscopic Structures (CIEMic).