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Local plasma-assisted etching of crystalline silicon by fine focused plasma jets provides a method for high accuracy computer controlled surface waviness and figure error correction as well as free form processing and manufacturing. We investigate a radio-frequency powered atmospheric pressure He/N2/CF4 plasma jet for the local chemical etching of silicon using fluorine as reactive plasma gas component. This plasma jet tool has a typical tool function width of about 0.5 to 1.8 mm and a material removal rate up to 0.068 mm3 min−1. The relationship between etching rate and plasma jet parameters is discussed in detail regarding gas composition, working distance, scan velocity and RF power. Surface roughness after etching was characterized using atomic force microscopy and white light interferometry. A strong smoothing effect was observed for etching rough silicon surfaces like wet chemically-etched silicon wafer backsides. Using the dwell-time algorithm for a deterministic surface machining by superposition of the local removal function of the plasma tool we show a fast and efficient way for manufacturing complex silicon structures. In this article we present two examples of surface processing using small local plasma jets