In this paper, a study of a mechatronic scanning system for application in the microbiology, microelectronics research, chemistry, etc. is presented. Integrated silicon micro electro mechanical system (MEMS) position sensor is used for monitoring the displacement of the scanning system. The utilized silicon MEMS sensors with sidewall embedded piezoresistors possess a number of key advantages such as high sensitivity, low noise and extremely low temperature dependence. Design of 2D scanning system with a travel range of 22 × 22 μm2 has been presented in present work. This system includes a Compliant Transmission Mechanism, (CTM) designed as a complex elastic mechanism, comprising four parallelograms. Computer aided desigh (CAD) model and finite element analysis (FEA) of the Compliant Transmission Mechanism mechanisms have been carried out. A prototype of the scanning system is fabricated, based on CAD model. An experimental set-up of an optical system and a correlation technique for digital image processing have been used for testing the scanning system prototype. Results of the experimental investigations of the prototyped scanning system are also presented.