Writing a molecularly imprinted polymer (MIP) by nano-fountain pen on surface-enhanced Raman scattering (SERS)-active surfaces resulted in site-controlled arrays of microdots of approximately 6–12μm in diameter. The monitoring of SERS spectra with a micro-Raman system enabled examining the uptake and release of the S-propranolol imprinting template and allowed imaging individual dots as well as multiple dots in an array, revealing the distribution of the imprinted polymer. This distribution was confirmed by atomic force microscopy, showing that even in dots of <300nm thickness, corresponding to MIP volumes of 0.5fl, significantly less than previously reported, the target analyte could be detected and identified. This study shows that nanolithography techniques combined with SERS might open the possibility of miniaturized arrayed MIP sensors with label-free, specific and quantitative detection.