It is difficult to deburr a micro-machined surface because the micro-features are easily damaged during the deburring processes. This paper proposes a new deburring process utilizing a magnetorheological fluid and applies it to the production of micromolds. A magnetorheological fluid is a functional fluid with a variable yield stress that is controlled by an external magnetic field. The proposed process utilizes two material removal mechanisms induced by the magnetorheological fluid flow. Extensive yielding of material is effective for deburring sheet-shaped burrs, and abrasive wear is effective for deburring protrusion-shaped burrs. A process model was developed to describe the effectiveness of each mechanism for specific burr geometries. The performance of the proposed method was verified experimentally. Metal burrs with a height of 200 μm and thickness of 1 μm were removed successfully with extensive yielding and abrasive wear. Burrs shorter than a few micrometers could be removed only by abrasive wear. The material removal behaviors of sheet-shaped and protrusion shaped burrs matched the proposed process model well.