## 1 Introduction  
Malachite green is often illegally used in aquaculture to prevent aquatic animals from being infected by parasites, fungi, and protozoa [1]. According to the results of animal experiments, malachite green can poison the liver of experimental animals, cause anemia and hyperhyroidism, and cause lung adenomas of experimental rats [2]. In order to avoid the harm of malachite green to human health, malachite green is prohibited from being used for aquaculture animals in the United States, and the UK [3]. According to the \"Standards for Residues of Animal Drugs\" of the Department of Health and Welfare, the residue of malachite green in aquatic products is \"not allowed to be detected\". The European Commission requires that detection methods be able to determine the sum of MG at the minimum performance limit of 2 ng/g (approximately 5.5 nM) [4]. The detection of malachite green residues is usually carried out at a sophisticated Laboratory using expensive equipments, such as liquid chromatography visible detection (LC-VIS) for routine screening and liquid chromatography mass spectrometry (LC-MS) for residue confirmation [1]. It is a time consuming and expensive process. There is a need for high throughput and cost-effective methods for screening these aquaculture products. Surface-enhanced Raman spectroscopy (SERS) technology has the potential to provide a very fast and sensitive method of detecting chemicals and biomolecules. It can be a solution for this unmet need. The 3D microstructure of the SERS substrate has a significant impact on the SERS signal. Studies have shown that the SERS signal can be enhanced by changing the 2D planar substrate into a 3D microstructure substrate, for example, silicon nanowire [5], and pyramid structure [6; 7; 8; 9]. This microstructured SERS substrate has a large surface area, therefore increases the number of effective hot spots, and further enhances the sensitivity of the SERS signal [10]. The microstructured silicon pyramid is particularly interesting one. Pyramid microstructure has been used in solar cells to improve the conversion efficiency of solar cells through its light trapping effect [11; 12; 13]. Due to its low process threshold and cost-effective performance, this is the most mature production process in the photovoltaic industry for decades. An anisotropic wet chemical etch is typically utilized to form a micro-sized pyramidal structure as a light-harvesting structure using different etch rates of silicon crystals at \(<\)100\(>\) and \(<\)111\(>\) surfaces [14]. It has been shown that a randomly sized pyramid array surface can have better light-harvesting efficiency and therefore a better absorption coefficient than planar and single sized pyramid array surfaces [15]. In some SERS studies [7; 8; 9], It has been proven that the Si pyramids can increase the amount of the hot spots by providing large surface area and create strong local electric field [9]. However, substrates with only 3D microstructures are not sufficient to generate strong SERS signals, and studies have shown that strong local surface plasmons (SERS hot spots) occur at the nano-gaps between noble metal nanostructures [9; 10]. Therefore, it is preferred that the SERS substrate can have both micron and nanostructures, which will greatly increase the SERS signal strength. In this study, we provide a facile method to produce SERS active substrates using simple steps and inexpensive costs. We use wet etching to create a pyramid-shaped large structure on a silicon wafer and then use the electrochemical process to create gold nanostructures on the pyramid surface. In previous studies, electrochemical surface treatment was mostly used to roughening the surface of bulk gold or bulk silver materials [16; 17]. In this study, we applied the electrochemical oxidation and reduction cycles to the gold thin film on the silicon micro-pyramid array, which leads to atomic restructuring of the gold thin film surface.