Shunts are often employed as internal medical devices for draining aberrant fluids from organs. However, depositions of calcification in the shunt walls lead to its failure, requiring frequent replacements. The current surgical procedures for implanting shunts are invasive. Methods: This paper introduces a novel, non-invasive approach for eliminating shunt deposits. In this non-invasive intervention, a swarm of magnetic nanoparticles (MNPs) guided by an external magnetic field removes the shunt deposition. A prototype device was fabricated to provide a proof of concept. MNPs were steered within the shunt channel containing calcification layers and successfully abraded the deposition layer. The proof-of-concept experiments used a moving magnetic field ranging from 0.1 to 0.3 T and a velocity between 1 to 12 cm/s. The average nanoparticle size was 45nm. Five diverse contact theories predicted the amount of wear and indentation depth created by the abrading microswarm. Results: Experimental results confirm that MNPs under a moving magnetic field can abrade shunt deposits. Also, there is a direct relation between the intensity of the magnetic field, the speed of magnet movement, and the rate of abrading the calcification deposits. The simulation results showed that the Hoeprich model deviated 12.1% from the experimental results and was the most suitable model. Conclusion & significance: This research has introduced a novel minimally invasive approach to remove shunt depositions that can reduce the number of revision surgeries and prevent surgical complications.