Microscopes have become a significant part of pathological study. Currently, motorized microscopes are enabled with horizontal and vertical movements, with the facility of fast response in acquiring images or videos from the slide. During microbial screening, viewing the specimen needs following a directional path viz., zig-zag, inward spiral, meander, and so forth. Even though the motorized movements are built-in, human intervention is required while screening. This leads to time delay in the scanning process and may leave some portions of the specimen unattended. In this proposed system, a programmable framework to define the scanning direction for the specimen and a firmware to control the microscopic stage is implemented, to enable customization of the scanning pattern without any human intervention during complete course of screening. The user can define the customized scanning pattern using two-dimensional (2D) graphics drawing primitives. The final drawing is converted into preparatory codes through a micro-computer numeric controlled software, which extracts the address information relating to the movement and direction of the stage. These X, Y directional information are fed into the machine control unit for activating the linear driving system, which has servo drives and motors to power the spindle for precise microscopic stage movement. The proposed system is cost effective and reduces the reliance on technicians in examining the whole slide. The system is also portable and can be attached to any conventional or fluorescence microscope. Some pre-defined scanning patterns have been tested for the stage movements and validated in this work.