An industrial linear stage is a device that is commonly used in robotics. To be precise, an industrial linear stage is an electro-mechanical system that includes a motor, electronics, flexible coupling, gear, ball screw, and precision linear bearing. A tight fit can provide better precision but also generates a difficult-to-model friction that is highly nonlinear and asymmetrical. Herein, this paper proposes an advanced trajectory controller based on a digital twin framework incorporated with artificial intelligence (AI), which can effectively control a precision linear stage. This framework offers several advantages: detection of abnormalities, estimation of performance, and selective control over any situation. The digital twin is developed via Matlab’s Simscape and runs concurrently having a real-time controller.