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We have developed a fabrication process for high-TC superconducting multilayer thin film structures using chemical-mechanical polishing (CMP). A multilayer high-TC flux transformer with a multi-turn input coil was fabricated using this technique. The flux transformer was coupled to a bicrystal dc SQUID in a flip-chip configuration that yielded a measured transformation coefficient of 1.6 nT/Φ0 corresponding to an equivalent magnetic field noise of 15 fT/HZ1/2 at 2 kHz. An excess 1/f noise was observed at frequencies below 2 kHz. This noise is attributed to the presence of (100)-oriented YBCO grains in the top electrode observed by transmission electron microscopy. Despite the presenceof the high 1/f noise, such a magnetometer can be used to improve the signal-to-noise ratio of low-field nuclear magnetic resonance (lf-NMR) systems. For this particular application, the low frequency noise is of less importance since the NMR signal at about 4 kHz is above the 1/f noise cut-off frequency of this device. The peculiarities of the CMP process, the multilayer flux transformer fabrication as well as whole magnetometer implementation will be presented in this report.